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Figueiredo BC, Dupont F, Portelli G, Costa TEJ, Custódio G, Paraizo MM, Komechen H, Gascuel H, Bottau M, Callea E, Percicote AP, Telles LG, Jendoubi M, Lalli E. AI-guided identification of risk variants for adrenocortical tumours in TP53 p.R337H carrier children: a genetic association study. LANCET REGIONAL HEALTH. AMERICAS 2024; 38:100863. [PMID: 39258234 PMCID: PMC11386259 DOI: 10.1016/j.lana.2024.100863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 09/12/2024]
Abstract
Background Adrenocortical tumours (ACT) in children are part of the Li-Fraumeni cancer spectrum and are frequently associated with a germline TP53 pathogenic variant. TP53 p.R337H is highly prevalent in the south and southeast of Brazil and predisposes to ACT with low penetrance. Thus, we aimed to investigate whether genetic variants exist which are associated with an increased risk of developing ACT in TP53 p.R337H carrier children. Methods A genetic association study was conducted in trios of children (14 girls, 7 boys) from southern Brazil carriers of TP53 p.R337H with (n = 18) or without (n = 3) ACT and their parents, one of whom also carries this pathogenic variant (discovery cohort). Results were confirmed in a validation cohort of TP53 p.R337H carriers with (n = 90; 68 girls, 22 boys) or without ACT (n = 302; 165 women, 137 men). Findings We analysed genomic data from whole exome sequencing of blood DNA from the trios. Using deep learning algorithms, according to a model where the affected child inherits from the non-carrier parent variant(s) increasing the risk of developing ACT, we found a significantly enriched representation of non-coding variants in genes involved in the cyclic AMP (cAMP) pathway known to be involved in adrenocortical tumorigenesis. One among those variants (rs2278986 in the SCARB1 gene) was confirmed to be significantly enriched in the validation cohort of TP53 p.R337H carriers with ACT compared to carriers without ACT (OR 1.858; 95% CI 1.146, 3.042, p = 0.01). Interpretation Profiling of the variant rs2278986 is a candidate for future confirmation and possible use as a tool for ACT risk stratification in TP53 p.R337H carriers. Funding Centre National de la Recherche Scientifique (CNRS), Behring Foundation, Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).
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Affiliation(s)
- Bonald C Figueiredo
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
- Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Florent Dupont
- Thales Services Numériques, Valbonne - Sophia Antipolis, France
| | | | | | - Gislaine Custódio
- Laboratório de Análises Clínicas, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Heloisa Komechen
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Hadrien Gascuel
- Thales Services Numériques, Valbonne - Sophia Antipolis, France
| | - Maxime Bottau
- Thales Services Numériques, Valbonne - Sophia Antipolis, France
| | - Elodie Callea
- Thales Services Numériques, Valbonne - Sophia Antipolis, France
| | | | | | - Mehdi Jendoubi
- Thales Services Numériques, Valbonne - Sophia Antipolis, France
| | - Enzo Lalli
- Institut de Pharmacologie Moléculaire et Cellulaire CNRS, Valbonne - Sophia Antipolis, France
- Inserm, Valbonne - Sophia Antipolis, France
- Université Côte d'Azur, Valbonne - Sophia Antipolis, France
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2
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Canesin LEC, Vilaça ST, Oliveira RRM, Al-Ajli F, Tracey A, Sims Y, Formenti G, Fedrigo O, Banhos A, Sanaiotti TM, Farias IP, Jarvis ED, Oliveira G, Hrbek T, Solferini V, Aleixo A. A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes. Sci Rep 2024; 14:19925. [PMID: 39261501 PMCID: PMC11390914 DOI: 10.1038/s41598-024-70305-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/14/2024] [Indexed: 09/13/2024] Open
Abstract
The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.
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Affiliation(s)
| | - Sibelle T Vilaça
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil
| | - Renato R M Oliveira
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil
| | - Farooq Al-Ajli
- Rockefeller University, New York, USA
- Katara Biodiversity Genomics Program, Katara Cultural Village Foundation, Doha, Qatar
| | | | - Ying Sims
- Rockefeller University, New York, USA
| | | | | | - Aureo Banhos
- Universidade Federal do Espírito Santo (UFES), Alegre, Brazil
| | | | | | - Erich D Jarvis
- Rockefeller University, New York, USA
- Howard Hughes Medical Institute (HHMI), New York, USA
| | - Guilherme Oliveira
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas (UFAM), Manaus, Brazil
- Trinity University, San Antonio, USA
| | - Vera Solferini
- Universidade Estadual de Campinas (Unicamp), Campinas, Brazil
| | - Alexandre Aleixo
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Belém, Brazil.
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3
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Morales AE, Burbrink FT, Segall M, Meza M, Munegowda C, Webala PW, Patterson BD, Thong VD, Ruedi M, Hiller M, Simmons NB. Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs. Mol Biol Evol 2024; 41:msae165. [PMID: 39116340 PMCID: PMC11371419 DOI: 10.1093/molbev/msae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 07/01/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Convergence offers an opportunity to explore to what extent evolution can be predictable when genomic composition and environmental triggers are similar. Here, we present an emergent model system to study convergent evolution in nature in a mammalian group, the bat genus Myotis. Three foraging strategies-gleaning, trawling, and aerial hawking, each characterized by different sets of phenotypic features-have evolved independently multiple times in different biogeographic regions in isolation for millions of years. To investigate the genomic basis of convergence and explore the functional genomic changes linked to ecomorphological convergence, we sequenced and annotated 17 new genomes and screened 16,426 genes for positive selection and associations between relative evolutionary rates and foraging strategies across 30 bat species representing all Myotis ecomorphs across geographic regions as well as among sister groups. We identify genomic changes that describe both phylogenetic and ecomorphological trends. We infer that colonization of new environments may have first required changes in genes linked to hearing sensory perception, followed by changes linked to fecundity and development, metabolism of carbohydrates, and heme degradation. These changes may be linked to prey acquisition and digestion and match phylogenetic trends. Our findings also suggest that the repeated evolution of ecomorphs does not always involve changes in the same genes but rather in genes with the same molecular functions such as developmental and cellular processes.
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Affiliation(s)
- Ariadna E Morales
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Department of Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Centre for Translational Biodiversity Genomics, Frankfurt am Main, Hessen, Germany
- Senckenberg Research Institute, Frankfurt am Main, Hessen, Germany
- Faculty of Biosciences, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Frank T Burbrink
- Department of Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
| | - Marion Segall
- Department of Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205, Muséum National d’Histoire Naturelle, CNRS, SU, EPHE, UA, CP 50, Paris, France
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Maria Meza
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Chetan Munegowda
- Centre for Translational Biodiversity Genomics, Frankfurt am Main, Hessen, Germany
- Senckenberg Research Institute, Frankfurt am Main, Hessen, Germany
- Faculty of Biosciences, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
| | - Bruce D Patterson
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, USA
| | - Vu Dinh Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Vietnam
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Geneva 1208, Switzerland
| | - Michael Hiller
- Centre for Translational Biodiversity Genomics, Frankfurt am Main, Hessen, Germany
- Senckenberg Research Institute, Frankfurt am Main, Hessen, Germany
- Faculty of Biosciences, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
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Kuhnert P, Loosli N, Brodard I, Lindtke D, Jores J. Resistance of zebu cattle (Bos indicus) to colonization by major ruminant hoof pathogens. Vet Microbiol 2024; 296:110184. [PMID: 38996749 DOI: 10.1016/j.vetmic.2024.110184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Zebu cattle (Bos indicus) is reported to be more resistant towards harmful environmental factors than taurine cattle (Bos taurus). A few hundred zebu cattle are kept in Switzerland and in contrast to the Swiss indigenous breeds, infectious hoof disease in zebu is not observed. Therefore, we compared the prevalence of three ruminant hoof pathogens in zebu and taurine cattle. These included Treponema spp., Fusobacterium necrophorum and Dichelobacter nodosus which are associated with bovine digital dermatitis (BDD), different bovine hoof diseases and ovine footrot, respectively. Interdigital swabs and punch biopsies from hind feet of slaughter animals were tested for the three pathogens by PCR. Sixty zebu from eight farms were compared to a convenience sample of 20 taurine cattle from 17 farms. Treponema spp. associated with BDD were not detected in zebu while 23 % of animals and 50 % of farms were positive for benign D. nodosus, with results indicating environmental contamination rather than colonization. Taurine cattle showed 35 % of animals and 41 % of farms positive for T. phagedenis while 90 % of animals and 94 % of farms were colonized by D. nodosus as indicated by a 500-fold higher bacterial load than in zebu. The difference in prevalence of the two pathogens between zebu and taurine cattle was highly significant. F. necrophorum was as well only detected in taurine cattle with values of 15 % of animals and 17.7 % of farms, being significantly different at the animal level. Furthermore, genetic analysis of Swiss zebu indicates high genomic diversity and clear separation from taurine cattle. This is the first evidence that zebu show resistance towards colonization by bacterial hoof pathogens in contrast to taurine cattle.
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Affiliation(s)
- Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, Bern 3012, Switzerland.
| | - Nadia Loosli
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, Bern 3012, Switzerland
| | - Isabelle Brodard
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, Bern 3012, Switzerland
| | | | - Joerg Jores
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, Bern 3012, Switzerland
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Mansueto L, Tandayu E, Mieog J, Garcia-de Heer L, Das R, Burn A, Mauleon R, Kretzschmar T. HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications. BMC Genomics 2024; 25:818. [PMID: 39210290 PMCID: PMC11363669 DOI: 10.1186/s12864-024-10734-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Cannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa. RESULTS The High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97% mean) and even distribution across the genome, designed to be highly informative (> 0.3 minor allele frequency) across both medicinal cannabis and industrial hemp gene pools. Average numbers of mismatch SNP between any two accessions were 251 for medicinal cannabis (N = 116) and 272 for industrial hemp (N = 87). Comparing HASCH data with corresponding GBS data on a collection of diverse C. sativa accessions demonstrated high concordance and resulted in comparable phylogenies and genetic distance matrices. Using HASCH on a segregating F2 population derived from a cross between a tetrahydrocannabinol (THC)-dominant and a cannabidiol (CBD)-dominant accession resulted in a genetic map consisting of 310 markers, comprising 10 linkage groups and a total size of 582.7 cM. Quantitative Trait Locus (QTL) mapping identified a major QTL for CBD content on chromosome 7, consistent with previous findings. CONCLUSION HASCH constitutes a versatile, easy to use and cost-effective genotyping solution for the rapidly growing Cannabis research community. It provides consistent genetic fingerprints of 1504 SNPs with wide applicability genetic resource management, quantitative genetics and breeding.
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Affiliation(s)
- Locedie Mansueto
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Erwin Tandayu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Jos Mieog
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Lennard Garcia-de Heer
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Rekhamani Das
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Adam Burn
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Ramil Mauleon
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
- International Rice Research Institute, Pili Drive, Los Banos, Laguna, Philippines
| | - Tobias Kretzschmar
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia.
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Lancaster MC, Chen HH, Shoemaker MB, Fleming MR, Strickland TL, Baker JT, Evans GF, Polikowsky HG, Samuels DC, Huff CD, Roden DM, Below JE. Detection of distant relatedness in biobanks to identify undiagnosed cases of Mendelian disease as applied to Long QT syndrome. Nat Commun 2024; 15:7507. [PMID: 39209900 PMCID: PMC11362435 DOI: 10.1038/s41467-024-51977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
Rare genetic diseases are typically studied in referral populations, resulting in underdiagnosis and biased assessment of penetrance and phenotype. To address this, we develop a generalizable method of genotype inference based on distant relatedness and deploy this to identify undiagnosed Type 5 Long QT Syndrome (LQT5) rare variant carriers in a non-referral population. We identify 9 LQT5 families referred to a single specialty clinic, each carrying p.Asp76Asn, the most common LQT5 variant. We uncover recent common ancestry and a single shared haplotype among probands. Application to a non-referral population of 69,819 BioVU biobank subjects identifies 22 additional subjects sharing this haplotype, which we confirm to carry p.Asp76Asn. Referral and non-referral carriers have prolonged QT interval corrected for heart rate (QTc) compared to controls, and, among carriers, the QTc polygenic score is independently associated with QTc prolongation. Thus, our innovative analysis of shared chromosomal segments identifies undiagnosed cases of genetic disease and refines the understanding of LQT5 penetrance and phenotype.
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Affiliation(s)
- Megan C Lancaster
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Hung-Hsin Chen
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11524, Taiwan
| | - M Benjamin Shoemaker
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Matthew R Fleming
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Teresa L Strickland
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - James T Baker
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Grahame F Evans
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Hannah G Polikowsky
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Chad D Huff
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dan M Roden
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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Luo X, Gu C, Gao S, Li M, Zhang H, Zhu S. Complete mitochondrial genome assembly of Zizania latifolia and comparative genome analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1381089. [PMID: 39184575 PMCID: PMC11341417 DOI: 10.3389/fpls.2024.1381089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/26/2024] [Indexed: 08/27/2024]
Abstract
Zizania latifolia (Griseb.) Turcz. ex Stapf has been cultivated as a popular aquatic vegetable in China due to its important nutritional, medicinal, ecological, and economic values. The complete mitochondrial genome (mitogenome) of Z. latifolia has not been previously studied and reported, which has hindered its molecular systematics and understanding of evolutionary processes. Here, we assembled the complete mitogenome of Z. latifolia and performed a comprehensive analysis including genome organization, repetitive sequences, RNA editing event, intercellular gene transfer, phylogenetic analysis, and comparative mitogenome analysis. The mitogenome of Z. latifolia was estimated to have a circular molecule of 392,219 bp and 58 genes consisting of three rRNA genes, 20 tRNA genes, and 35 protein-coding genes (PCGs). There were 46 and 20 simple sequence repeats (SSRs) with different motifs identified from the mitogenome and chloroplast genome of Z. latifolia, respectively. Furthermore, 49 homologous fragments were observed to transfer from the chloroplast genome to the mitogenome of Z. latifolia, accounting for 47,500 bp, presenting 12.1% of the whole mitogenome. In addition, there were 11 gene-containing homologous regions between the mitogenome and chloroplast genome of Z. latifolia. Also, approximately 85% of fragments from the mitogenome were duplicated in the Z. latifolia nuclear genome. Selection pressure analysis revealed that most of the mitochondrial genes were highly conserved except for ccmFc, ccmFn, matR, rps1, and rps3. A total of 93 RNA editing sites were found in the PCGs of the mitogenome. Z. latifolia and Oryza minuta are the most closely related, as shown by collinear analysis and the phylogenetic analysis. We found that repeat sequences and foreign sequences in the mitogenomes of Oryzoideae plants were associated with genome rearrangements. In general, the availability of the Z. latifolia mitogenome will contribute valuable information to our understanding of the molecular and genomic aspects of Zizania.
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Affiliation(s)
| | | | | | | | | | - Shidong Zhu
- College of Horticulture, Anhui Agricultural University, Hefei, China
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Aagaard A, Bechsgaard J, Sørensen JG, Sandfeld T, Settepani V, Bird TL, Lund MB, Malmos KG, Falck-Rasmussen K, Darolti I, Nielsen KL, Johannsen M, Vosegaard T, Tregenza T, Verhoeven KJF, Mank JE, Schramm A, Bilde T. Molecular Mechanisms of Temperature Tolerance Plasticity in an Arthropod. Genome Biol Evol 2024; 16:evae165. [PMID: 39058286 DOI: 10.1093/gbe/evae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
How species thrive in a wide range of environments is a major focus of evolutionary biology. For many species, limited genetic diversity or gene flow among habitats means that phenotypic plasticity must play an important role in their capacity to tolerate environmental heterogeneity and to colonize new habitats. However, we have a limited understanding of the molecular components that govern plasticity in ecologically relevant phenotypes. We examined this hypothesis in a spider species (Stegodyphus dumicola) with extremely low species-wide genetic diversity that nevertheless occupies a broad range of thermal environments. We determined phenotypic responses to temperature stress in individuals from four climatic zones using common garden acclimation experiments to disentangle phenotypic plasticity from genetic adaptations. Simultaneously, we created data sets on multiple molecular modalities: the genome, the transcriptome, the methylome, the metabolome, and the bacterial microbiome to determine associations with phenotypic responses. Analyses of phenotypic and molecular associations reveal that acclimation responses in the transcriptome and metabolome correlate with patterns of phenotypic plasticity in temperature tolerance. Surprisingly, genes whose expression seemed to be involved in plasticity in temperature tolerance were generally highly methylated contradicting the idea that DNA methylation stabilizes gene expression. This suggests that the function of DNA methylation in invertebrates varies not only among species but also among genes. The bacterial microbiome was stable across the acclimation period; combined with our previous demonstrations that the microbiome is temporally stable in wild populations, this is convincing evidence that the microbiome does not facilitate plasticity in temperature tolerance. Our results suggest that population-specific variation in temperature tolerance among acclimation temperatures appears to result from the evolution of plasticity in mainly gene expression.
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Affiliation(s)
- Anne Aagaard
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Jesper Bechsgaard
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Jesper Givskov Sørensen
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Tobias Sandfeld
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Virginia Settepani
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Tharina L Bird
- General Entomology, DITSONG: National Museum of Natural History, Pretoria, South Africa
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Arachnology and Myriapodology, National Museum of Namibia, Windhoek, Namibia
| | - Marie Braad Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Kirsten Gade Malmos
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | - Kasper Falck-Rasmussen
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Mogens Johannsen
- Department of Forensic Medicine, Aarhus University, Aarhus N, Denmark
| | - Thomas Vosegaard
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Tom Tregenza
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn TR109FE, UK
| | - Koen J F Verhoeven
- Terrestrial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, The Netherlands
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Trine Bilde
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn TR109FE, UK
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Osborne A, Mańko E, Waweru H, Kaneko A, Kita K, Campino S, Gitaka J, Clark TG. Plasmodium falciparum population dynamics in East Africa and genomic surveillance along the Kenya-Uganda border. Sci Rep 2024; 14:18051. [PMID: 39103358 PMCID: PMC11300580 DOI: 10.1038/s41598-024-67623-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/15/2024] [Indexed: 08/07/2024] Open
Abstract
East African countries accounted for ~ 10% of all malaria prevalence worldwide in 2022, with an estimated 23.8 million cases and > 53,000 deaths. Despite recent increases in malaria incidence, high-resolution genome-wide analyses of Plasmodium parasite populations are sparse in Kenya, Tanzania, and Uganda. The Kenyan-Ugandan border region is a particular concern, with Uganda confirming the emergence and spread of artemisinin resistant P. falciparum parasites. To establish genomic surveillance along the Kenyan-Ugandan border and analyse P. falciparum population dynamics within East Africa, we generated whole-genome sequencing (WGS) data for 38 parasites from Bungoma, Western Kenya. These sequences were integrated into a genomic analysis of available East African isolate data (n = 599) and revealed parasite subpopulations with distinct genetic structure and diverse ancestral origins. Ancestral admixture analysis of these subpopulations alongside isolates from across Africa (n = 365) suggested potential independent ancestral populations from other major African populations. Within isolates from Western Kenya, the prevalence of biomarkers associated with chloroquine resistance (e.g. Pfcrt K76T) were significantly reduced compared to wider East African populations and a single isolate contained the PfK13 V568I variant, potentially linked to reduced susceptibility to artemisinin. Overall, our work provides baseline WGS data and analysis for future malaria genomic surveillance in the region.
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Affiliation(s)
- Ashley Osborne
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Emilia Mańko
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Harrison Waweru
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Akira Kaneko
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya.
- Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya.
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
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10
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Li Q, Fu C, Yang B, Yu H, He H, Xu Q, Miao W, Liu R, Chen W, Zhang Z, Zou X, Hu B, Ou L. Stem lodging Resistance-1 controls stem strength by positively regulating the biosynthesis of cell wall components in Capsicum annuum L. HORTICULTURE RESEARCH 2024; 11:uhae169. [PMID: 39135730 PMCID: PMC11317896 DOI: 10.1093/hr/uhae169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/14/2024] [Indexed: 08/15/2024]
Abstract
Lodging presents a significant challenge in cultivating high-yield crops with extensive above-ground biomass, yet the molecular mechanisms underlying this phenomenon in the Solanaceae family remain largely unexplored. In this study, we identified a gene, CaSLR1 (Capsicum annuum Stem Lodging Resistance 1), which encodes a MYELOBLASTOSIS (MYB) family transcription factor, from a lodging-affected C. annuum EMS mutant. The suppression of CaSLR1 expression in pepper led to notable stem lodging, reduced thickness of the secondary cell wall, and decreased stem strength. A similar phenotype was observed in tomato with the knockdown of SlMYB61, the orthologous gene to CaSLR1. Further investigations demonstrated that CaNAC6, a gene involved in secondary cell wall (SCW) formation, is co-expressed with CaSLR1 and acts as a positive regulator of its expression, as confirmed through yeast one-hybrid, dual-luciferase reporter assays, and electrophoretic mobility shift assays. These findings elucidate the CaNAC6-CaSLR1 module that contributes to lodging resistance, emphasizing the critical role of CaSLR1 in the lodging resistance regulatory network.
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Affiliation(s)
- Qing Li
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Yuelushan Lab, Changsha 410128, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Canfang Fu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Yuelushan Lab, Changsha 410128, China
| | - Bozhi Yang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Yuelushan Lab, Changsha 410128, China
| | - Huiyang Yu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Yuelushan Lab, Changsha 410128, China
| | - Huan He
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Yuelushan Lab, Changsha 410128, China
| | - Qing Xu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Yuelushan Lab, Changsha 410128, China
| | - Wu Miao
- Hunan Xiangyan Seed Industry Co., Ltd, Changsha, 410100, China
| | - Rongyun Liu
- Hunan Xiangyan Seed Industry Co., Ltd, Changsha, 410100, China
| | - Wenchao Chen
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Zhuqing Zhang
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Xuexiao Zou
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Yuelushan Lab, Changsha 410128, China
| | - Bowen Hu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Yuelushan Lab, Changsha 410128, China
| | - Lijun Ou
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Yuelushan Lab, Changsha 410128, China
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11
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Chen M, Dai S, Chen D, Zhu P, Feng N, Zheng D. Comparative Analysis Highlights Uniconazole's Efficacy in Enhancing the Cold Stress Tolerance of Mung Beans by Targeting Photosynthetic Pathways. PLANTS (BASEL, SWITZERLAND) 2024; 13:1885. [PMID: 39065416 PMCID: PMC11280120 DOI: 10.3390/plants13141885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024]
Abstract
Soybean (Glycine max) and mung bean (Vigna radiata) are key legumes with global importance, but their mechanisms for coping with cold stress-a major challenge in agriculture-have not been thoroughly investigated, especially in a comparative study. This research aimed to fill this gap by examining how these two major legumes respond differently to cold stress and exploring the role of uniconazole, a potential stress mitigator. Our comprehensive approach involved transcriptomic and metabolomic analyses, revealing distinct responses between soybean and mung bean under cold stress conditions. Notably, uniconazole was found to significantly enhance cold tolerance in mung bean by upregulating genes associated with photosynthesis, while its impact on soybean was either negligible or adverse. To further understand the molecular interactions, we utilized advanced machine learning algorithms for protein structure prediction, focusing on photosynthetic pathways. This enabled us to identify LOC106780309 as a direct binding target for uniconazole, confirmed through isothermal titration calorimetry. This research establishes a new comparative approach to explore how soybean and mung bean adapt to cold stress, offers key insights to improve the hardiness of legumes against environmental challenges, and contributes to sustainable agricultural practices and food security.
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Affiliation(s)
- Mingming Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
- Shenzhen Research Institute of Guangdong Ocean University, Guangdong Ocean University, Shenzhen 518108, China
| | - Shuangfeng Dai
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
- Shenzhen Research Institute of Guangdong Ocean University, Guangdong Ocean University, Shenzhen 518108, China
| | - Daming Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
| | - Peiyi Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
- Shenzhen Research Institute of Guangdong Ocean University, Guangdong Ocean University, Shenzhen 518108, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
- Shenzhen Research Institute of Guangdong Ocean University, Guangdong Ocean University, Shenzhen 518108, China
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12
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Gopalan SS, Perry BW, Francioli YZ, Schield DR, Guss HD, Bernstein JM, Ballard K, Smith CF, Saviola AJ, Adams RH, Mackessy SP, Castoe TA. Diverse Gene Regulatory Mechanisms Alter Rattlesnake Venom Gene Expression at Fine Evolutionary Scales. Genome Biol Evol 2024; 16:evae110. [PMID: 38753011 PMCID: PMC11243404 DOI: 10.1093/gbe/evae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 07/13/2024] Open
Abstract
Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic diversity evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole-genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce differences in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive diversity in venom phenotypes. Our results illustrate that differences in chromatin and genotype at regulatory elements play major roles in modulating expression. However, we also find that enhancer deletions, differences in transcription factor expression, and variation in activity of the insulator protein CTCF also likely impact venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation.
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Affiliation(s)
- Siddharth S Gopalan
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Yannick Z Francioli
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Drew R Schield
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Hannah D Guss
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Justin M Bernstein
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Kaas Ballard
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Cara F Smith
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Richard H Adams
- Department of Entomology and Plant Pathology, University of Arkansas Agricultural Experimental Station, University of Arkansas, Fayetteville, AR 72701, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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13
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Krysztopa-Grzybowska K, Lach J, Polak M, Strapagiel D, Dziadek J, Olszewski M, Zasada AA, Darlińska A, Lutyńska A, Augustynowicz-Kopeć E. The whole genome sequence of Polish vaccine strain Mycobacterium bovis BCG Moreau. Microbiol Spectr 2024; 12:e0425923. [PMID: 38757975 PMCID: PMC11237378 DOI: 10.1128/spectrum.04259-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Abstract
Currently, tuberculosis immunoprophylaxis is based solely on Bacillus Calmette-Guérin (BCG) vaccination, and some of the new potential tuberculosis vaccines are based on the BCG genome. Therefore, it is reasonable to analyze the genomes of individual BCG substrains. The aim of this study was the genetic characterization of the BCG-Moreau Polish (PL) strain used for the production of the BCG vaccine in Poland since 1955. Sequencing of different BCG lots showed that the strain was stable over a period of 59 years. As a result of comparison, BCG-Moreau PL with BCG-Moreau Rio de Janeiro (RDJ) 143 single nucleotide polymorphisms (SNPs) and 32 insertion/deletion mutations (INDELs) were identified. However, the verification of these mutations showed that the most significant were accumulated in the BCG-Moreau RDJ genome. The mutations unique to the Polish strain genome are 1 SNP and 2 INDEL. The strategy of combining short-read sequencing with long-read sequencing is currently the most optimal approach for sequencing bacterial genomes. With this approach, the only available genomic sequence of BCG-Moreau PL was obtained. This sequence will primarily be a reference point in the genetic control of the stability of the vaccine strain in the future. The results enrich knowledge about the microevolution and attenuation of the BCG vaccine substrains. IMPORTANCE The whole genome sequence obtained is the only genomic sequence of the strain that has been used for vaccine production in Poland since 1955. Sequencing of different BCG lots showed that the strain was stable over a period of 59 years. The comprehensive genomic analysis performed not only enriches knowledge about the microevolution and attenuation of the BCG vaccine substrains but also enables the utilization of identified markers as a reference point in the genetic control and identity tests of the stability of the vaccine strain in the future.
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Affiliation(s)
- Katarzyna Krysztopa-Grzybowska
- Department of Sera and Vaccines Evaluation, National Institute of Public Health NIH – National Research Institute, Warsaw, Poland
| | - Jakub Lach
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Maciej Polak
- Department of Sera and Vaccines Evaluation, National Institute of Public Health NIH – National Research Institute, Warsaw, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jaroslaw Dziadek
- Mycobacterium Genetics and Physiology Unit, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Marcin Olszewski
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Aleksandra A. Zasada
- Department of Sera and Vaccines Evaluation, National Institute of Public Health NIH – National Research Institute, Warsaw, Poland
| | - Aniela Darlińska
- Department of Sera and Vaccines Evaluation, National Institute of Public Health NIH – National Research Institute, Warsaw, Poland
| | - Anna Lutyńska
- Department of Medical Biology, National Institute of Cardiology, Warsaw, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
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14
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Zhang T, Wang Z, Li Y, Zhou B, Liu Y, Li J, Wang R, Lv Q, Li C, Zhang Y, Su R. Genetic diversity and population structure in five Inner Mongolia cashmere goat populations using whole-genome genotyping. Anim Biosci 2024; 37:1168-1176. [PMID: 38575127 PMCID: PMC11222833 DOI: 10.5713/ab.23.0424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/03/2023] [Accepted: 01/26/2024] [Indexed: 04/06/2024] Open
Abstract
OBJECTIVE As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future. METHODS Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations. RESULTS Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations. CONCLUSION The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future.
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Affiliation(s)
- Tao Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
| | - Yaming Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
| | - Bohan Zhou
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
| | - Yifan Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
| | - Jinquan Li
- Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
| | - Qi Lv
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
| | - Chun Li
- College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, Inner Mongolia Autonomous Region, 028000,
China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
- Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018,
China
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15
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Tavakoli N, Gibney D, Aluru S. GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants. J Comput Biol 2024; 31:616-637. [PMID: 38990757 DOI: 10.1089/cmb.2024.0601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
Modern genomic datasets, like those generated under the 1000 Genome Project, contain millions of variants belonging to known haplotypes. Although these datasets are more representative than a single reference sequence and can alleviate issues like reference bias, they are significantly more computationally burdensome to work with, often involving large-indexed genome graph data structures for tasks such as read mapping. The construction, preprocessing, and mapping algorithms can require substantial computational resources depending on the size of these variant sets. Moreover, the accuracy of mapping algorithms has been shown to decrease when working with complete variant sets. Therefore, a drastically reduced set of variants that preserves important properties of the original set is desirable. This work provides a technique for finding a minimal subset of variants S such that for given parameters α and δ, all substrings up to length α in the haplotypes are guaranteed to be still alignable to the appropriate locations with either Hamming or edit distance at most δ, using only S . Our contributions include showing the NP-hardness and inapproximability of these optimization problems and providing Integer Linear Programming (ILP) formulations. Our edit distance ILP formulation carefully decomposes the problem according to variant locations, which allows it to scale to support all of chromosome 22's variants from the 1000 Genome Project. Our experiments also demonstrate a significant reduction in the number of variants. For example, for moderately long reads, e.g., α = 1000, over 75% of the variants can be removed while preserving read mappability with edit distance at most one.
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Affiliation(s)
- Neda Tavakoli
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Gxeorgia, USA
| | - Daniel Gibney
- Department of Computer Science, University of Texas at Dallas, Richardson, Texas, USA
| | - Srinivas Aluru
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Gxeorgia, USA
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16
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Bianco L, Fontana P, Marchesini A, Torre S, Moser M, Piazza S, Alessandri S, Pavese V, Pollegioni P, Vernesi C, Malnoy M, Torello Marinoni D, Murolo S, Dondini L, Mattioni C, Botta R, Sebastiani F, Micheletti D, Palmieri L. The de novo, chromosome-level genome assembly of the sweet chestnut (Castanea sativa Mill.) Cv. Marrone Di Chiusa Pesio. BMC Genom Data 2024; 25:64. [PMID: 38909221 PMCID: PMC11193896 DOI: 10.1186/s12863-024-01245-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024] Open
Abstract
OBJECTIVES The sweet chestnut Castanea sativa Mill. is the only native Castanea species in Europe, and it is a tree of high economic value that provides appreciated fruits and valuable wood. In this study, we assembled a high-quality nuclear genome of the ancient Italian chestnut variety 'Marrone di Chiusa Pesio' using a combination of Oxford Nanopore Technologies long reads, whole-genome and Omni-C Illumina short reads. DATA DESCRIPTION The genome was assembled into 238 scaffolds with an N50 size of 21.8 Mb and an N80 size of 7.1 Mb for a total assembled sequence of 750 Mb. The BUSCO assessment revealed that 98.6% of the genome matched the embryophyte dataset, highlighting good completeness of the genetic space. After chromosome-level scaffolding, 12 chromosomes with a total length of 715.8 and 713.0 Mb were constructed for haplotype 1 and haplotype 2, respectively. The repetitive elements represented 37.3% and 37.4% of the total assembled genome in haplotype 1 and haplotype 2, respectively. A total of 57,653 and 58,146 genes were predicted in the two haplotypes, and approximately 73% of the genes were functionally annotated using the EggNOG-mapper. The assembled genome will be a valuable resource and reference for future chestnut breeding and genetic improvement.
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Affiliation(s)
- Luca Bianco
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Alexis Marchesini
- Research Institute on Terrestrial Ecosystem, National Research Council, Via Marconi 2, Porano, TR, 05010, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Sara Torre
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino FI, Italy
| | - Mirko Moser
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Stefano Piazza
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Sara Alessandri
- Dept. of Agricultural and Food Sciences, University of Bologna, Via Zamboni 33, Bologna, BO, 40126, Italy
| | - Vera Pavese
- Dept. of Agricultural, Forest and Food Sci, University of Turin, L.go P. Braccini 2, Grugliasco, TO, 10095, Italy
| | - Paola Pollegioni
- Research Institute on Terrestrial Ecosystem, National Research Council, Via Marconi 2, Porano, TR, 05010, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Cristiano Vernesi
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Mickael Malnoy
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Daniela Torello Marinoni
- Dept. of Agricultural, Forest and Food Sci, University of Turin, L.go P. Braccini 2, Grugliasco, TO, 10095, Italy
| | - Sergio Murolo
- Dep. of Agricultural, Food and Env.Sci, Marche Polytechnic University, via Brecce Bianche, Ancona, AN, 60131, Italy
| | - Luca Dondini
- Dept. of Agricultural and Food Sciences, University of Bologna, Via Zamboni 33, Bologna, BO, 40126, Italy
| | - Claudia Mattioni
- Research Institute on Terrestrial Ecosystem, National Research Council, Via Marconi 2, Porano, TR, 05010, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Roberto Botta
- Dept. of Agricultural, Forest and Food Sci, University of Turin, L.go P. Braccini 2, Grugliasco, TO, 10095, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino FI, Italy
| | - Diego Micheletti
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Luisa Palmieri
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy.
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17
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Villamor-Payà M, Sanchiz-Calvo M, Smak J, Pais L, Sud M, Shankavaram U, Lovgren AK, Austin-Tse C, Ganesh VS, Gay M, Vilaseca M, Arauz-Garofalo G, Palenzuela L, VanNoy G, O’Donnell-Luria A, Stracker TH. De novo TLK1 and MDM1 mutations in a patient with a neurodevelopmental disorder and immunodeficiency. iScience 2024; 27:109984. [PMID: 38868186 PMCID: PMC11166698 DOI: 10.1016/j.isci.2024.109984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/08/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
The Tousled-like kinases 1 and 2 (TLK1/TLK2) regulate DNA replication, repair and chromatin maintenance. TLK2 variants underlie the neurodevelopmental disorder (NDD) 'Intellectual Disability, Autosomal Dominant 57' (MRD57), characterized by intellectual disability and microcephaly. Several TLK1 variants have been reported in NDDs but their functional significance is unknown. A male patient presenting with ID, seizures, global developmental delay, hypothyroidism, and primary immunodeficiency was determined to have a heterozygous TLK1 variant (c.1435C>G, p.Q479E), as well as a mutation in MDM1 (c.1197dupT, p.K400∗). Cells expressing TLK1 p.Q479E exhibited reduced cytokine responses and elevated DNA damage, but not increased radiation sensitivity or DNA repair defects. The TLK1 p.Q479E variant impaired kinase activity but not proximal protein interactions. Our study provides the first functional characterization of NDD-associated TLK1 variants and suggests that, such as TLK2, TLK1 variants may impact development in multiple tissues and should be considered in the diagnosis of rare NDDs.
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Affiliation(s)
- Marina Villamor-Payà
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - María Sanchiz-Calvo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Jordann Smak
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - Lynn Pais
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Malika Sud
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Uma Shankavaram
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
| | - Alysia Kern Lovgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay S. Ganesh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Gianluca Arauz-Garofalo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Lluís Palenzuela
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Grace VanNoy
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne O’Donnell-Luria
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Travis H. Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, MD 20892, USA
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18
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Davison A, Chowdhury M, Johansen M, Uliano-Silva M, Blaxter M. High heteroplasmy is associated with low mitochondrial copy number and selection against non-synonymous mutations in the snail Cepaea nemoralis. BMC Genomics 2024; 25:596. [PMID: 38872121 DOI: 10.1186/s12864-024-10505-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
Molluscan mitochondrial genomes are unusual because they show wide variation in size, radical genome rearrangements and frequently show high variation (> 10%) within species. As progress in understanding this variation has been limited, we used whole genome sequencing of a six-generation matriline of the terrestrial snail Cepaea nemoralis, as well as whole genome sequences from wild-collected C. nemoralis, the sister species C. hortensis, and multiple other snail species to explore the origins of mitochondrial DNA (mtDNA) variation. The main finding is that a high rate of SNP heteroplasmy in somatic tissue was negatively correlated with mtDNA copy number in both Cepaea species. In individuals with under ten mtDNA copies per nuclear genome, more than 10% of all positions were heteroplasmic, with evidence for transmission of this heteroplasmy through the germline. Further analyses showed evidence for purifying selection acting on non-synonymous mutations, even at low frequency of the rare allele, especially in cytochrome oxidase subunit 1 and cytochrome b. The mtDNA of some individuals of Cepaea nemoralis contained a length heteroplasmy, including up to 12 direct repeat copies of tRNA-Val, with 24 copies in another snail, Candidula rugosiuscula, and repeats of tRNA-Thr in C. hortensis. These repeats likely arise due to error prone replication but are not correlated with mitochondrial copy number in C. nemoralis. Overall, the findings provide key insights into mechanisms of replication, mutation and evolution in molluscan mtDNA, and so will inform wider studies on the biology and evolution of mtDNA across animal phyla.
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Affiliation(s)
- Angus Davison
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Mehrab Chowdhury
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Margrethe Johansen
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Marcela Uliano-Silva
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
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19
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Manyara D, Sánchez-García M, Montoliu-Nerin M, Rosling A. Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198. G3 (BETHESDA, MD.) 2024; 14:jkae074. [PMID: 38656424 DOI: 10.1093/g3journal/jkae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.
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Affiliation(s)
- David Manyara
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
| | - Marisol Sánchez-García
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Merce Montoliu-Nerin
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Madrid 28223, Spain
| | - Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
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20
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Li J, Fan Y, Li N, Guo Y, Wang W, Feng K, He W, Li F, Huang J, Xu Y, Xiao L, Feng Y. Comparative genomics analysis reveals sequence characteristics potentially related to host preference in Cryptosporidium xiaoi. Int J Parasitol 2024; 54:379-390. [PMID: 38492779 DOI: 10.1016/j.ijpara.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Cryptosporidium spp. are important diarrhea-associated pathogens in humans and livestock. Among the known species, Cryptosporidium xiaoi, which causes cryptosporidiosis in sheep and goats, was previously recognized as a genotype of the bovine-specific Cryptosporidium bovis based on their high sequence identity in the ssrRNA gene. However, the lack of genomic data has limited characterization of the genetic differences between the two closely related species. In this study, we sequenced the genomes of two C. xiaoi isolates and performed comparative genomic analysis to identify the sequence uniqueness of this ovine-adapted species compared with other Cryptosporidium spp. Our results showed that C. xiaoi is genetically related to C. bovis as shown by their 95.8% genomic identity and similar gene content. Consistent with this, both C. xiaoi and C. bovis appear to have fewer genes encoding mitochondrial metabolic enzymes and invasion-related protein families. However, they appear to possess several species-specific genes. Further analysis indicates that the sequence differences between these two Cryptosporidium spp. are mainly in 24 highly polymorphic genes, half of which are located in the subtelomeric regions. Some of these subtelomeric genes encode secretory proteins that have undergone positive selection. In addition, the genomes of two C. xiaoi isolates, identified as subtypes XXIIIf and XXIIIh, share 99.9% nucleotide sequence identity, with six highly divergent genes encoding putative secretory proteins. Therefore, these species-specific genes and sequence polymorphism in subtelomeric genes probably contribute to the different host preference of C. xiaoi and C. bovis.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yingying Fan
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Weijian Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Kangli Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Wei He
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Falei Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Jianbo Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yanhua Xu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
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21
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Li G, Liu Y, Feng X, Diao S, Zhong Z, Li B, Teng J, Zhang W, Zeng H, Cai X, Gao Y, Liu X, Yuan X, Li J, Zhang Z. Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations. Int J Mol Sci 2024; 25:5689. [PMID: 38891877 PMCID: PMC11171535 DOI: 10.3390/ijms25115689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
The domestic pig (Sus scrofa) and its subfamilies have experienced long-term and extensive gene flow, particularly in Southeast Asia. Here, we analyzed 236 pigs, focusing on Yunnan indigenous, European commercial, East Asian, and Southeast Asian breeds, using the Pig Genomics Reference Panel (PGRP v1) of Pig Genotype-Tissue Expression (PigGTEx) to investigate gene flow and associated complex traits by integrating multiple database resources. In this study, we discovered evidence of admixtures from European pigs into the genome of Yunnan indigenous pigs. Additionally, we hypothesized that a potential conceptual gene flow route that may have contributed to the genetic composition of the Diannan small-ear pig is a gene exchange from the Vietnamese pig. Based on the most stringent gene introgression scan using the fd statistic, we identified three specific loci on chromosome 8, ranging from 51.65 to 52.45 Mb, which exhibited strong signatures of selection and harbored the NAF1, NPY1R, and NPY5R genes. These genes are associated with complex traits, such as fat mass, immunity, and litter weight, in pigs, as supported by multiple bio-functionalization databases. We utilized multiple databases to explore the potential dynamics of genetic exchange in Southeast Asian pig populations and elucidated specific gene functionalities.
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Affiliation(s)
- Guangzhen Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Yuqiang Liu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xueyan Feng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Shuqi Diao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Zhanming Zhong
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Bolang Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Jinyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Wenjing Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Haonan Zeng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xiaodian Cai
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Yahui Gao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Xiaolong Yuan
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
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22
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Zhou X, Qiang C, Chen L, Qing D, Huang J, Li J, Pan Y. The Landscape of Presence/Absence Variations during the Improvement of Rice. Genes (Basel) 2024; 15:645. [PMID: 38790274 PMCID: PMC11120952 DOI: 10.3390/genes15050645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Rice is one of the most important staple crops in the world; therefore, the improvement of rice holds great significance for enhancing agricultural production and addressing food security challenges. Although there have been numerous studies on the role of single-nucleotide polymorphisms (SNPs) in rice improvement with the development of next-generation sequencing technologies, research on the role of presence/absence variations (PAVs) in the improvement of rice is limited. In particular, there is a scarcity of studies exploring the traits and genes that may be affected by PAVs in rice. Here, we extracted PAVs utilizing resequencing data from 148 improved rice varieties distributed in Asia. We detected a total of 33,220 PAVs and found that the number of variations decreased gradually as the length of the PAVs increased. The number of PAVs was the highest on chromosome 1. Furthermore, we identified a 6 Mb hotspot region on chromosome 11 containing 1091 PAVs in which there were 29 genes related to defense responses. By conducting a genome-wide association study (GWAS) using PAV variation data and phenotypic data for five traits (flowering time, plant height, flag leaf length, flag leaf width, and panicle number) across all materials, we identified 186 significantly associated PAVs involving 20 cloned genes. A haplotype analysis and expression analysis of candidate genes revealed that important genes might be affected by PAVs, such as the flowering time gene OsSFL1 and the flag leaf width gene NAL1. Our work investigated the pattern in PAVs and explored important PAV key functional genes associated with agronomic traits. Consequently, these results provide potential and exploitable genetic resources for rice breeding.
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Affiliation(s)
- Xia Zhou
- Urban Construction School, Beijing City University, Beijing 101300, China;
| | - Chenggen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Lei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.C.); (D.Q.); (J.H.)
| | - Dongjin Qing
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.C.); (D.Q.); (J.H.)
| | - Juan Huang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.C.); (D.Q.); (J.H.)
| | - Jilong Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.C.); (D.Q.); (J.H.)
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23
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Shen C, Lu Q, Yang D, Zhang X, Huang X, Li R, Que Z, Chen N. Genome-wide identification analysis in wild-type Solanum pinnatisectum reveals some genes defending against Phytophthora infestans. Front Genet 2024; 15:1379784. [PMID: 38812971 PMCID: PMC11134371 DOI: 10.3389/fgene.2024.1379784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024] Open
Abstract
Solanum pinnatisectum exhibits strong resistance to late blight caused by Phytophthora infestans but only an incomplete genome assembly based on short Illumina reads has been published. In this study, we generated the first chromosome-level draft genome for the wild-type potato species S. pinnatisectum in China using Oxford Nanopore technology sequencing and Hi-C technology. The high-quality assembled genome size is 664 Mb with a scaffold N50 value of 49.17 Mb, of which 65.87% was occupied by repetitive sequences, and predominant long terminal repeats (42.51% of the entire genome). The genome of S. pinnatisectum was predicted to contain 34,245 genes, of which 99.34% were functionally annotated. Moreover, 303 NBS-coding disease resistance (R) genes were predicted in the S. pinnatisectum genome to investigate the potential mechanisms of resistance to late blight disease. The high-quality chromosome-level reference genome of S. pinnatisectum is expected to provide potential valuable resources for intensively and effectively investigating molecular breeding and genetic research in the future.
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Affiliation(s)
- Chunxiu Shen
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Qineng Lu
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Di Yang
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | | | | | - Rungen Li
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Zhiqun Que
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Na Chen
- Jiangxi Key Laboratory of Crop Growth and Development Regulation, College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
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24
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Gutiérrez-Valencia J, Zervakis PI, Postel Z, Fracassetti M, Losvik A, Mehrabi S, Bunikis I, Soler L, Hughes PW, Désamoré A, Laenen B, Abdelaziz M, Pettersson OV, Arroyo J, Slotte T. Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum. Mol Biol Evol 2024; 41:msae087. [PMID: 38709782 PMCID: PMC11114476 DOI: 10.1093/molbev/msae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/22/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024] Open
Abstract
Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.
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Affiliation(s)
- Juanita Gutiérrez-Valencia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Panagiotis-Ioannis Zervakis
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Zoé Postel
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marco Fracassetti
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aleksandra Losvik
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Sara Mehrabi
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Uppsala Genome Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, Uppsala University, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - P William Hughes
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aurélie Désamoré
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, Uppsala Genome Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juan Arroyo
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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25
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Chelban V, Aksnes H, Maroofian R, LaMonica LC, Seabra L, Siggervåg A, Devic P, Shamseldin HE, Vandrovcova J, Murphy D, Richard AC, Quenez O, Bonnevalle A, Zanetti MN, Kaiyrzhanov R, Salpietro V, Efthymiou S, Schottlaender LV, Morsy H, Scardamaglia A, Tariq A, Pagnamenta AT, Pennavaria A, Krogstad LS, Bekkelund ÅK, Caiella A, Glomnes N, Brønstad KM, Tury S, Moreno De Luca A, Boland-Auge A, Olaso R, Deleuze JF, Anheim M, Cretin B, Vona B, Alajlan F, Abdulwahab F, Battini JL, İpek R, Bauer P, Zifarelli G, Gungor S, Kurul SH, Lochmuller H, Da'as SI, Fakhro KA, Gómez-Pascual A, Botía JA, Wood NW, Horvath R, Ernst AM, Rothman JE, McEntagart M, Crow YJ, Alkuraya FS, Nicolas G, Arnesen T, Houlden H. Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications. Nat Commun 2024; 15:2269. [PMID: 38480682 PMCID: PMC10937998 DOI: 10.1038/s41467-024-46354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Primary familial brain calcification (PFBC) is characterized by calcium deposition in the brain, causing progressive movement disorders, psychiatric symptoms, and cognitive decline. PFBC is a heterogeneous disorder currently linked to variants in six different genes, but most patients remain genetically undiagnosed. Here, we identify biallelic NAA60 variants in ten individuals from seven families with autosomal recessive PFBC. The NAA60 variants lead to loss-of-function with lack of protein N-terminal (Nt)-acetylation activity. We show that the phosphate importer SLC20A2 is a substrate of NAA60 in vitro. In cells, loss of NAA60 caused reduced surface levels of SLC20A2 and a reduction in extracellular phosphate uptake. This study establishes NAA60 as a causal gene for PFBC, provides a possible biochemical explanation of its disease-causing mechanisms and underscores NAA60-mediated Nt-acetylation of transmembrane proteins as a fundamental process for healthy neurobiological functioning.
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Affiliation(s)
- Viorica Chelban
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.
- Neurobiology and Medical Genetics Laboratory, "Nicolae Testemitanu" State University of Medicine and Pharmacy, 165, Stefan cel Mare si Sfant Boulevard, MD, 2004, Chisinau, Republic of Moldova.
| | - Henriette Aksnes
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Lauren C LaMonica
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Luis Seabra
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR 1163, Paris, France
| | | | - Perrine Devic
- Hospices Civils de Lyon, Groupement Hospitalier Sud, Service d'Explorations Fonctionnelles Neurologiques, Lyon, France
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Anne-Claire Richard
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - Olivier Quenez
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - Antoine Bonnevalle
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - M Natalia Zanetti
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- South Kazakhstan Medical Academy Shymkent, Shymkent, 160019, Kazakhstan
| | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Lucia V Schottlaender
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral, Av. Juan Domingo Perón 1500, B1629AHJ, Pilar, Argentina
- Instituto de medicina genómica (IMeG), Hospital Universitario Austral, Universidad Austral, Av. Juan Domingo Perón 1500, B1629AHJ, Pilar, Argentina
| | - Heba Morsy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Annarita Scardamaglia
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Ambreen Tariq
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Alistair T Pagnamenta
- Oxford NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Ajia Pennavaria
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Liv S Krogstad
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Åse K Bekkelund
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Alessia Caiella
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nina Glomnes
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5020, Bergen, Norway
| | | | - Sandrine Tury
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, Montpellier, France
| | - Andrés Moreno De Luca
- Department of Radiology, Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
- Department of Radiology, Neuroradiology Section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Anne Boland-Auge
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Mathieu Anheim
- Neurology Department, Strasbourg University Hospital, Strasbourg, France
- Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg, France
- INSERM-U964; CNRS-UMR7104, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Benjamin Cretin
- Neurology Department, Strasbourg University Hospital, Strasbourg, France
- Strasbourg Federation of Translational Medicine (FMTS), Strasbourg University, Strasbourg, France
- INSERM-U964; CNRS-UMR7104, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Fahad Alajlan
- Department of Neuroscience Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jean-Luc Battini
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, Montpellier, France
| | - Rojan İpek
- Paediatric Neurology, Faculty of Medicine, Dicle University, Diyarbakır, Turkey
| | - Peter Bauer
- Centogene GmbH, Am Strande 7, 18055, Rostock, Germany
| | | | - Serdal Gungor
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Pediatrics, Division of Pediatric Neurology, Malatya, Turkey
| | - Semra Hiz Kurul
- Dokuz Eylul University, School of Medicine, Department of Paediatric Neurology, Izmir, Turkey
| | - Hanns Lochmuller
- Children's Hospital of Eastern Ontario Research Institute and Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Sahar I Da'as
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Weill Cornell Medical College, Doha, Qatar
| | - Alicia Gómez-Pascual
- Department of Information and Communications Engineering, University of Murcia, Campus Espinardo, 30100, Murcia, Spain
| | - Juan A Botía
- Department of Information and Communications Engineering, University of Murcia, Campus Espinardo, 30100, Murcia, Spain
| | - Nicholas W Wood
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Neurogenetics Laboratory, The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Andreas M Ernst
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - James E Rothman
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Meriel McEntagart
- Medical Genetics Department, St George's University Hospitals, London, SWI7 0RE, UK
| | - Yanick J Crow
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR 1163, Paris, France
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245, CHU Rouen, Department of Genetics and CNRMAJ, F-76000, Rouen, France
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.
- Neurogenetics Laboratory, The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK.
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26
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Wei Z, Zhang L, Gao L, Chen J, Peng L, Yang L. Chromosome-level genome assembly and annotation of the Yunling cattle with PacBio and Hi-C sequencing data. Sci Data 2024; 11:233. [PMID: 38395911 PMCID: PMC10891105 DOI: 10.1038/s41597-024-03066-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Yunling cattle is a new breed of beef cattle bred in Yunnan Province, China. It is bred by crossing the Brahman, the Murray Grey and the Yunnan Yellow cattle. Yunling cattle can adapt to the tropical and subtropical climate environment, and has good reproductive ability and growth speed under high temperature and high humidity conditions, it also has strong resistance to internal and external parasites and with good beef performance. In this study, we generated a high-quality chromosome-level genome assembly of a male Yunling cattle using a combination of short reads sequencing, PacBio HiFi sequencing and Hi-C scaffolding technologies. The genome assembly(3.09 Gb) is anchored to 31 chromosomes(29 autosomes plus one X and Y), with a contig N50 of 35.97 Mb and a scaffold N50 of 112.01 Mb. It contains 1.62 Gb of repetitive sequences and 20,660 protein-coding genes. This first construction of the Yunling cattle genome provides a valuable genetic resource that will facilitate further study of the genetic diversity of bovine species and accelerate Yunling cattle breeding efforts.
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Affiliation(s)
- Zaichao Wei
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- College of Big Data, Baoshan University, Baoshan, China
| | - Lilian Zhang
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Lutao Gao
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Jian Chen
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Lin Peng
- College of Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China
| | - Linnan Yang
- College of Big Data, Yunnan Agricultural University, Kunming, China.
- Yunnan Engineering Technology Research Center of Agricultural Big Data, Kunming, China.
- Yunnan Engineering Research Center for Big Data Intelligent Information Processing of Green Agricultural Products, Kunming, China.
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27
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Wang P, Jin M, Wu C, Peng Y, He Y, Wang H, Xiao Y. Population genomics of Agrotis segetum provide insights into the local adaptive evolution of agricultural pests. BMC Biol 2024; 22:42. [PMID: 38378556 PMCID: PMC10877822 DOI: 10.1186/s12915-024-01844-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND The adaptive mechanisms of agricultural pests are the key to understanding the evolution of the pests and to developing new control strategies. However, there are few studies on the genetic basis of adaptations of agricultural pests. The turnip moth, Agrotis segetum (Lepidoptera: Noctuidae) is an important underground pest that affects a wide range of host plants and has a strong capacity to adapt to new environments. It is thus a good model for studying the adaptive evolution of pest species. RESULTS We assembled a high-quality reference genome of A. segetum using PacBio reads. Then, we constructed a variation map of A. segetum by resequencing 98 individuals collected from six natural populations in China. The analysis of the population structure showed that all individuals were divided into four well-differentiated populations, corresponding to their geographical distribution. Selective sweep analysis and environmental association studies showed that candidate genes associated with local adaptation were functionally correlated with detoxification metabolism and glucose metabolism. CONCLUSIONS Our study of A. segetum has provided insights into the genetic mechanisms of local adaptation and evolution; it has also produced genetic resources for developing new pest management strategies.
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Affiliation(s)
- Ping Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan university, Shenzhen, 518000, China
| | - Minghui Jin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yanjin He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan university, Shenzhen, 518000, China
| | - Hanyue Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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28
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Foley NM, Harris AJ, Bredemeyer KR, Ruedi M, Puechmaille SJ, Teeling EC, Criscitiello MF, Murphy WJ. Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation. CELL GENOMICS 2024; 4:100482. [PMID: 38237599 PMCID: PMC10879000 DOI: 10.1016/j.xgen.2023.100482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/17/2023] [Accepted: 12/10/2023] [Indexed: 02/17/2024]
Abstract
The emergence of COVID-19 and severe acute respiratory syndrome (SARS) has prioritized understanding bats' viral tolerance. Myotis bats are exceptionally species rich and have evolved viral tolerance. They also exhibit swarming, a cryptic behavior where large, multi-species assemblages gather for mating, which has been hypothesized to promote interspecific hybridization. To resolve the coevolution of genome architecture and their unusual antiviral tolerance, we undertook a phylogenomic analysis of 60 Old World Myotis genomes. We demonstrate an extensive history of introgressive hybridization that has replaced the species phylogeny across 17%-93% of the genome except for pericentromeric regions of macrochromosomes. Introgression tracts were enriched on microchromosome regions containing key antiviral pathway genes overexpressed during viral challenge experiments. Together, these results suggest that the unusual Myotis karyotype may have evolved to selectively position immune-related genes in high recombining genomic regions prone to introgression of divergent alleles, including a diversity of interleukin loci responsible for the release of pro-inflammatory cytokines.
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Affiliation(s)
- Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Route de Malagnou 1, BP 6434, 1211 Geneva 6, Switzerland
| | - Sebastien J Puechmaille
- Institut des Sciences de l'Évolution, Montpellier (ISEM), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France; Institut Universitaire de France, Paris, France
| | - Emma C Teeling
- School of Biology and Environmental, Science, Science Centre West, University College Dublin, Belfield, Ireland
| | - Michael F Criscitiello
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA; Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA.
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29
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Liang J, Tang M, Chen L, Wang W, Liang X. Oxidative stress resistance prompts pyrroloquinoline quinone biosynthesis in Hyphomicrobium denitrificans H4-45. Appl Microbiol Biotechnol 2024; 108:204. [PMID: 38349428 PMCID: PMC10864529 DOI: 10.1007/s00253-024-13053-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/15/2024]
Abstract
Pyrroloquinoline quinone (PQQ) is a natural antioxidant with diverse applications in food and pharmaceutical industries. A lot of effort has been devoted toward the discovery of PQQ high-producing microbial species and characterization of biosynthesis, but it is still challenging to achieve a high PQQ yield. In this study, a combined strategy of random mutagenesis and adaptive laboratory evolution (ALE) with fermentation optimization was applied to improve PQQ production in Hyphomicrobium denitrificans H4-45. A mutant strain AE-9 was obtained after nearly 400 generations of UV-LiCl mutagenesis, followed by an ALE process, which was conducted with a consecutive increase of oxidative stress generated by kanamycin, sodium sulfide, and potassium tellurite. In the flask culture condition, the PQQ production in mutant strain AE-9 had an 80.4% increase, and the cell density increased by 14.9% when compared with that of the initial strain H4-45. Moreover, batch and fed-batch fermentation processes were optimized to further improve PQQ production by pH control strategy, methanol and H2O2 feed flow, and segmented fermentation process. Finally, the highest PQQ production and productivity of the mutant strain AE-9 reached 307 mg/L and 4.26 mg/L/h in a 3.7-L bioreactor, respectively. Whole genome sequencing analysis showed that genetic mutations in the ftfL gene and thiC gene might contribute to improving PQQ production by enhancing methanol consumption and cell growth in the AE-9 strain. Our study provided a systematic strategy to obtain a PQQ high-producing mutant strain and achieve high production of PQQ in fermentation. These practical methods could be applicable to improve the production of other antioxidant compounds with uncleared regulation mechanisms. KEY POINTS: • Improvement of PQQ production by UV-LiCl mutagenesis combined with adaptive laboratory evolution (ALE) and fermentation optimization. • A consecutive increase of oxidative stress could be used as the antagonistic factor for ALE to enhance PQQ production. • Mutations in the ftfL gene and thiC gene indicated that PQQ production might be increased by enhancing methanol consumption and cell growth.
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Affiliation(s)
- Jiale Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Mingjie Tang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Lang Chen
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Wenjie Wang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
| | - Xinle Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
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Friis G, Smith EG, Lovelock CE, Ortega A, Marshell A, Duarte CM, Burt JA. Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula. Mol Ecol 2024; 33:e17260. [PMID: 38197286 DOI: 10.1111/mec.17260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 11/13/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure correlating with geographic distance and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modelling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, suggesting the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among populations. Genetic-environment association analyses revealed high levels of adaptive divergence and detected signs of multi-loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.
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Affiliation(s)
- Guillermo Friis
- Center for Genomics and Systems Biology (CGSB) and Mubadala ACCESS Center, New York University - Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Catherine E Lovelock
- School of Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Alejandra Ortega
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - John A Burt
- Center for Genomics and Systems Biology (CGSB) and Mubadala ACCESS Center, New York University - Abu Dhabi, Abu Dhabi, United Arab Emirates
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31
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Barazandeh M, Kriti D, Fickel J, Nislow C. The Addis Ababa Lions: Whole-Genome Sequencing of a Rare and Precious Population. Genome Biol Evol 2024; 16:evae021. [PMID: 38302110 PMCID: PMC10871700 DOI: 10.1093/gbe/evae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
Lions are widely known as charismatic predators that once roamed across the globe, but their populations have been greatly affected by environmental factors and human activities over the last 150 yr. Of particular interest is the Addis Ababa lion population, which has been maintained in captivity at around 20 individuals for over 75 yr, while many wild African lion populations have become extinct. In order to understand the molecular features of this unique population, we conducted a whole-genome sequencing study on 15 Addis Ababa lions and detected 4.5 million distinct genomic variants compared with the reference African lion genome. Using functional annotation, we identified several genes with mutations that potentially impact various traits such as mane color, body size, reproduction, gastrointestinal functions, cardiovascular processes, and sensory perception. These findings offer valuable insights into the genetics of this threatened lion population.
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Affiliation(s)
- Marjan Barazandeh
- Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jörns Fickel
- Institute for Biochemistry and Biology, University Potsdam, Potsdam, Germany
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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Holt JM, Saunders CT, Rowell WJ, Kronenberg Z, Wenger AM, Eberle M. HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing. Bioinformatics 2024; 40:btae042. [PMID: 38269623 PMCID: PMC10868326 DOI: 10.1093/bioinformatics/btae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/13/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
MOTIVATION In diploid organisms, phasing is the problem of assigning the alleles at heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing provide long, accurate observations that can be used as the basis for both calling and phasing variants. HiFi reads also excel at calling larger classes of variation, such as structural or tandem repeat variants. However, current phasing tools typically only phase small variants, leaving larger variants unphased. RESULTS We developed HiPhase, a tool that jointly phases SNVs, indels, structural, and tandem repeat variants. The main benefits of HiPhase are (i) dual mode allele assignment for detecting large variants, (ii) a novel application of the A*-algorithm to phasing, and (iii) logic allowing phase blocks to span breaks caused by alignment issues around reference gaps and homozygous deletions. In our assessment, HiPhase produced an average phase block NG50 of 480 kb with 929 switchflip errors and fully phased 93.8% of genes, improving over the current state of the art. Additionally, HiPhase jointly phases SNVs, indels, structural, and tandem repeat variants and includes innate multi-threading, statistics gathering, and concurrent phased alignment output generation. AVAILABILITY AND IMPLEMENTATION HiPhase is available as source code and a pre-compiled Linux binary with a user guide at https://github.com/PacificBiosciences/HiPhase.
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Affiliation(s)
- James M Holt
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
| | | | - William J Rowell
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
| | - Zev Kronenberg
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
| | - Aaron M Wenger
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
| | - Michael Eberle
- Computational Biology, PacBio, 1305 O’Brien Drive, Menlo Park, CA 94025, United States
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Zhang W, Yang Y, Hua S, Ruan Q, Li D, Wang L, Wang X, Wen X, Liu X, Meng Z. Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara. Sci Data 2024; 11:151. [PMID: 38296995 PMCID: PMC10830450 DOI: 10.1038/s41597-024-02989-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Epinephelus awoara, as known as yellow grouper, is a significant economic marine fish that has been bred artificially in China. However, the genetic structure and evolutionary history of yellow grouper remains largely unknown. Here, this work presents the high-quality chromosome-level genome assembly of yellow grouper using PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The 984.48 Mb chromosome-level genome of yellow grouper was assembled, with a contig N50 length of 39.77 Mb and scaffold N50 length of 41.39 Mb. Approximately 99.76% of assembled sequences were anchored into 24 pseudo-chromosomes with the assistance of Hi-C reads. Furthermore, approximately 41.17% of the genome was composed of repetitive elements. In total, 24,541 protein-coding genes were predicted, of which 22,509 (91.72%) genes were functionally annotated. The highly accurate, chromosome-level reference genome assembly and annotation are crucial to the understanding of population genetic structure, adaptive evolution and speciation of the yellow grouper.
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Affiliation(s)
- Weiwei Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Tropical Marine Fish Germplasm Innovation and Utilization, Ministry of Agriculture and Rural Affairs, Sanya, 570000, China
- Hainan Engineering Research Center for Germplasm Innovation and Utilization, Sanya, 570000, China
| | - Sijie Hua
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qingxin Ruan
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Duo Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Le Wang
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore City, 119077, Singapore
| | - Xi Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xin Wen
- School of Marine Biology and Fisheries, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, 519000, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, 519000, China.
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Hao Q, Liu M, Daulatabad SV, Gaffari S, Song YJ, Srivastava R, Bhaskar S, Moitra A, Mangan H, Tseng E, Gilmore RB, Frier SM, Chen X, Wang C, Huang S, Chamberlain S, Jin H, Korlach J, McStay B, Sinha S, Janga SC, Prasanth SG, Prasanth KV. Monoallelically expressed noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression. eLife 2024; 13:e80684. [PMID: 38240312 PMCID: PMC10852677 DOI: 10.7554/elife.80684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
Out of the several hundred copies of rRNA genes arranged in the nucleolar organizing regions (NOR) of the five human acrocentric chromosomes, ~50% remain transcriptionally inactive. NOR-associated sequences and epigenetic modifications contribute to the differential expression of rRNAs. However, the mechanism(s) controlling the dosage of active versus inactive rRNA genes within each NOR in mammals is yet to be determined. We have discovered a family of ncRNAs, SNULs (Single NUcleolus Localized RNA), which form constrained sub-nucleolar territories on individual NORs and influence rRNA expression. Individual members of the SNULs monoallelically associate with specific NOR-containing chromosomes. SNULs share sequence similarity to pre-rRNA and localize in the sub-nucleolar compartment with pre-rRNA. Finally, SNULs control rRNA expression by influencing pre-rRNA sorting to the DFC compartment and pre-rRNA processing. Our study discovered a novel class of ncRNAs influencing rRNA expression by forming constrained nucleolar territories on individual NORs.
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Affiliation(s)
- Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Minxue Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Swapna Vidhur Daulatabad
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUIIndianapolisUnited States
| | - Saba Gaffari
- Department of Computer Science, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUIIndianapolisUnited States
| | - Shivang Bhaskar
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Anurupa Moitra
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Hazel Mangan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | | | - Rachel B Gilmore
- Department of Genetics and Genome Sciences, University of Connecticut School of MedicineFarmingtonUnited States
| | | | - Xin Chen
- Department of Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Chengliang Wang
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern UniversityChicagoUnited States
| | - Stormy Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut School of MedicineFarmingtonUnited States
| | - Hong Jin
- Department of Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | | | - Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Department of Biomedical Engineering, Georgia TechAtlantaUnited States
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUIIndianapolisUnited States
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Cancer Center at Illinois, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Cancer Center at Illinois, University of Illinois at Urbana-ChampaignUrbanaUnited States
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Li H, Peng Y, Wu C, Li Z, Zou L, Mao K, Ping J, Buck R, Monahan S, Sethuraman A, Xiao Y. Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens. INSECT SCIENCE 2024. [PMID: 38204333 DOI: 10.1111/1744-7917.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China. Here, 3 highly differentiated subpopulations were discovered using high-quality single-nucleotide polymorphism and structural variant datasets across China, corresponding to northern, southern China regions, and the Yunnan-Guizhou Plateau, with significant patterns of isolation by geographic and environmental distances. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations. Selective sweep analyses estimated strong selection at insect cuticle glycine-rich cuticular protein genes which are associated with enhanced desiccation adaptability in the northern group, and at the histone-lysine-N-methyltransferase gene associated with range expansion and local adaptation in the Shandong population. Our findings have significant implications for the development of effective strategies to control this pest.
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Affiliation(s)
- Hongran Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Chao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Zhimin Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Luming Zou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Kaikai Mao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Junfen Ping
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Ryan Buck
- Department of Biology, San Diego State University, CA, USA
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Scott Monahan
- Department of Biology, San Diego State University, CA, USA
| | | | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
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Crombie TA, McKeown R, Moya ND, Evans K, Widmayer S, LaGrassa V, Roman N, Tursunova O, Zhang G, Gibson S, Buchanan C, Roberto N, Vieira R, Tanny R, Andersen E. CaeNDR, the Caenorhabditis Natural Diversity Resource. Nucleic Acids Res 2024; 52:D850-D858. [PMID: 37855690 PMCID: PMC10767927 DOI: 10.1093/nar/gkad887] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/30/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Studies of model organisms have provided important insights into how natural genetic differences shape trait variation. These discoveries are driven by the growing availability of genomes and the expansive experimental toolkits afforded to researchers using these species. For example, Caenorhabditis elegans is increasingly being used to identify and measure the effects of natural genetic variants on traits using quantitative genetics. Since 2016, the C. elegans Natural Diversity Resource (CeNDR) has facilitated many of these studies by providing an archive of wild strains, genome-wide sequence and variant data for each strain, and a genome-wide association (GWA) mapping portal for the C. elegans community. Here, we present an updated platform, the Caenorhabditis Natural Diversity Resource (CaeNDR), that enables quantitative genetics and genomics studies across the three Caenorhabditis species: C. elegans, C. briggsae and C. tropicalis. The CaeNDR platform hosts several databases that are continually updated by the addition of new strains, whole-genome sequence data and annotated variants. Additionally, CaeNDR provides new interactive tools to explore natural variation and enable GWA mappings. All CaeNDR data and tools are accessible through a freely available web portal located at caendr.org.
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Affiliation(s)
- Timothy A Crombie
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ryan McKeown
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Nicolas D Moya
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Cell, Molecular, Developmental biology, and Biophysics Graduate Program, ohns Hopkins University, Baltimore, MD, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Samuel J Widmayer
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Vincent LaGrassa
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Natalie Roman
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Orzu Tursunova
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sophia B Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Claire M Buchanan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Rodolfo Vieira
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Robyn E Tanny
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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37
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Genovese G, Rockweiler NB, Gorman BR, Bigdeli TB, Pato MT, Pato CN, Ichihara K, McCarroll SA. BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies. Bioinformatics 2024; 40:btae038. [PMID: 38261650 PMCID: PMC10832354 DOI: 10.1093/bioinformatics/btae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/07/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024] Open
Abstract
MOTIVATION Many genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and improved, researchers are faced with either realigning raw sequence data using the updated coordinate system or converting legacy datasets to the updated coordinate system to be able to combine results with newer datasets. Currently available tools to perform the conversion of genetic variants have numerous shortcomings, including poor support for indels and multi-allelic variants, that lead to a higher rate of variants being dropped or incorrectly converted. As a result, many researchers continue to work with and publish using legacy genomic coordinates. RESULTS Here we present BCFtools/liftover, a tool to convert genomic coordinates across genome assemblies for variants encoded in the variant call format with improved support for indels represented by different reference alleles across genome assemblies and full support for multi-allelic variants. It further supports variant annotation fields updates whenever the reference allele changes across genome assemblies. The tool has the lowest rate of variants being dropped with an order of magnitude less indels dropped or incorrectly converted and is an order of magnitude faster than other tools typically used for the same task. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies as well as summary statistics from genome-wide association studies tied to legacy genome assemblies. AVAILABILITY AND IMPLEMENTATION The tool is written in C and freely available under the MIT open source license as a BCFtools plugin available at http://github.com/freeseek/score.
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Affiliation(s)
- Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Nicole B Rockweiler
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Bryan R Gorman
- Center for Data and Computational Sciences, VA Boston HealthCare System, Boston, MA 02130, United States
- Booz Allen Hamilton Inc, McLean, VA 22102, United States
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
- Cooperative Studies Program, VA New York Harbor Healthcare System, Brooklyn, NY 11209, United States
| | - Michelle T Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, United States
| | - Carlos N Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, United States
| | - Kiku Ichihara
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
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Xia X, Liu L, Cai K, Song X, Yue W, Wang J. A splicing site change between exon 5 and 6 of the nuclear-encoded chloroplast-localized HvYGL8 gene results in reduced chlorophyll content and plant height in barley. FRONTIERS IN PLANT SCIENCE 2023; 14:1327246. [PMID: 38192692 PMCID: PMC10773589 DOI: 10.3389/fpls.2023.1327246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
The chloroplast is an important cellular organelle and metabolic hub, which is not only responsible for plant photosynthesis but is also involved in the de novo biosynthesis of pigments, fatty acids, and hormone metabolisms. Several genes that are responsible for rice leaf color variations have been reported to be directly or indirectly involved in chlorophyll biosynthesis and chloroplast development, whereas a few genes have been functionally confirmed to be responsible for leaf color changes in barley at the molecular level. In this study, we obtained a yellow leaf and dwarf ygl8 mutant from the progeny of Morex (a variety of barley) seeds treated with EMS. We performed bulked-segregant analysis (BSA) and RNA-seq analysis and targeted a UMP kinase encoding gene, YGL8, which generated a splicing site change between exon 5 and 6 of YGL8 due to a G to A single-nucleotide transition in the 5th exon/intron junction in the ygl8 mutant. The splicing site change between exon 5 and 6 of YGL8 had no effects on chloroplast subcellular localization but resulted in an additional loop in the UMP kinase domain, which might disturb the access of the substrates. On one hand, the splicing site change between exon 5 and 6 of YGL8 downregulated the transcriptional expression of chloroplast-encoded genes and chlorophyll-biosynthesis-related genes in a temperature-dependent manner in the ygl8 mutant. On the other hand, the downregulation of bioactive GA-biosynthesis-related GA20ox genes and cell-wall-cellulose-biosynthesis-related CesA genes was also observed in the ygl8 mutant, which led to a reduction in plant height. Our study will facilitate the understanding of the regulation of leaf color and plant height in barley.
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Affiliation(s)
- Xue Xia
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
- College of Advanced Agricultural Sciences, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Lei Liu
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
| | - Kangfeng Cai
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
| | - Xiujuan Song
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
- College of Advanced Agricultural Sciences, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Wenhao Yue
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
| | - Junmei Wang
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou, China
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Wang Y, Xu J, Lan T, Zhou C, Liu P. The loss of neoantigens is an important reason for immune escape in multiple myeloma patients with high intratumor heterogeneity. Cancer Med 2023; 12:21651-21665. [PMID: 37965778 PMCID: PMC10757111 DOI: 10.1002/cam4.6721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/30/2023] [Accepted: 10/04/2023] [Indexed: 11/16/2023] Open
Abstract
OBJECTIVES Intratumor heterogeneity (ITH) is an important factor for clinical outcomes in patients with multiple myeloma (MM). High ITH has been proven to be a key reason for tumor immune escape and treatment resistance. Neoantigens are thought to be associated with ITH, but the specific correlation and functional basis for this remains unclear. METHODS We study this question through the whole-exome sequencing (WES) data from 43 high ITH newly diagnosed MM patients in our center. Mutant allele tumor heterogeneity (MATH) was conducted to quantify ITH. The cutoff value for high intratumor heterogeneity was determined by comparing MATH of different kinds of tumors. NeoPredPipe was performed to predict neoantigens and binding affinity. RESULTS Compared to other tumors, MM has a relatively low tumor mutation burden but a high ITH. Patients with high MATH had significantly shorter progression-free survival times than those with low MATH (p = 0.001). In high ITH samples, there is a decrease in strong-binding neoantigens (p = 0.019). The loss of strong-binding neoantigens is a key factor for insensitivity to therapy (p = 0.015). Loss of heterozygosity in HLA was not observed. In addition, patients with fewer neoantigens loss had higher rates of disease remission (p = 0.047). CD8 + T cells (p = 0.012) and NK cells (p = 0.011) decreased significantly in patients with high neoantigens loss rate. A prediction model based on neoantigens was built to evaluate the strength of immune escape. CONCLUSION The loss of strong-binding neoantigens explains why tumors with high ITH have a higher degree of immune escape and may be feasible for deciding the clinical treatment of MM.
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Affiliation(s)
- Yue Wang
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Jiadai Xu
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Tianwei Lan
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Chi Zhou
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Peng Liu
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
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Sarel-Gallily R, Keshet G, Kinreich S, Haim-Abadi G, Benvenisty N. EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq. Nat Protoc 2023; 18:3881-3917. [PMID: 37914783 DOI: 10.1038/s41596-023-00898-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/28/2023] [Indexed: 11/03/2023]
Abstract
Human pluripotent stem cells (hPSCs) hold a central role in studying human development, in disease modeling and in regenerative medicine. These cells not only acquire genetic modifications when kept in culture, but they may also harbor epigenetic aberrations, mainly involving parental imprinting and X-chromosome inactivation. Here we present a detailed bioinformatic protocol for detecting such aberrations using RNA sequencing data. We provide a pipeline designed to process and analyze RNA sequencing data for the identification of abnormal biallelic expression of imprinted genes, and thus detect loss of imprinting. Furthermore, we show how to differentiate among X-chromosome inactivation, full activation and aberrant erosion of X chromosome in female hPSCs. In addition to providing bioinformatic tools, we discuss the impact of such epigenetic variations in hPSCs on their utility for various purposes. This pipeline can be used by any user with basic understanding of the Linux command line. It is available on GitHub as a software container ( https://github.com/Gal-Keshet/EpiTyping ) and produces reliable results in 1-4 d.
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Affiliation(s)
- Roni Sarel-Gallily
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gal Keshet
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Shay Kinreich
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Guy Haim-Abadi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Barr K, Bossu CM, Bay RA, Anderson EC, Belthoff J, Trulio LA, Chromczak D, Wisinski CL, Smith TB, Ruegg KC. Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management. Evol Appl 2023; 16:1889-1900. [PMID: 38143900 PMCID: PMC10739168 DOI: 10.1111/eva.13600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 12/26/2023] Open
Abstract
Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation-by-distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation-by-distance, and substantially lower inbreeding. Using genotype-environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.
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Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Christen M. Bossu
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCaliforniaUSA
| | - Eric C. Anderson
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Jim Belthoff
- Raptor Research Center and Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Lynne A. Trulio
- Department of Environmental StudiesSan José State UniversitySan JoseCaliforniaUSA
| | - Debra Chromczak
- Burrowing Owl Researcher & ConsultantRiegelsvillePennsylvaniaUSA
| | | | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Kristen C. Ruegg
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
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Vickos U, Camasta M, Grandi N, Scognamiglio S, Schindler T, Belizaire MRD, Lango-Yaya E, Koyaweda GW, Senzongo O, Pounguinza S, Estimé KKJF, N’yetobouko S, Gadia CLB, Feiganazoui DA, Le Faou A, Orsini M, Perno CF, Zinzula L, Rafaï CD. COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome. Viruses 2023; 15:2309. [PMID: 38140550 PMCID: PMC10748234 DOI: 10.3390/v15122309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.
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Affiliation(s)
- Ulrich Vickos
- Department of Diagnostic and Laboratory Medicine, UOC Microbiology and Immunology Diagnostics, Children’s Hospital Bambino Gesù, IRCCS, 00118 Rome, Italy;
- Department of Medicine, Infectious and Tropical Diseases, Sino-Central African Amitié Hospital, Bangui 94045, Central African Republic
| | - Marianna Camasta
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
| | - Sante Scognamiglio
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland;
- Department of Medical Parasitology and Infection Biology, University of Basel, 4051 Basel, Switzerland
| | | | - Ernest Lango-Yaya
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Giscard Wilfried Koyaweda
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Oscar Senzongo
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Simon Pounguinza
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Kaleb Kandou Jephté Francis Estimé
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Stephanie N’yetobouko
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Christelle Luce Bobossi Gadia
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Dominos-Alfred Feiganazoui
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Alain Le Faou
- EA 3452 CITHEFOR, Campus Brabois Santé, 54500 Vandœuvre-lès-Nancy, France;
- Faculty of Medicine, Maieutic and Health Sciences, University of Lorraine, Pole Brabois Santé, 54500 Nancy, France
| | - Massimiliano Orsini
- General and Experimental Microbiology, Laboratory of Microbial Ecology and Genomics of Microorganisms, Experimental Zooprophylactic Institute of the Venezie (IZSVe), 35020 Legnaro, Italy;
| | - Carlo Federico Perno
- Department of Diagnostic and Laboratory Medicine, UOC Microbiology and Immunology Diagnostics, Children’s Hospital Bambino Gesù, IRCCS, 00118 Rome, Italy;
| | - Luca Zinzula
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Clotaire Donatien Rafaï
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
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43
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Li J, Mayor P, Robles MLS, Greenwood AD. The complete mitochondrial genome of the lowland paca ( Cuniculus paca) and its phylogenetic relationship with other New World hystricognath rodents. Mitochondrial DNA B Resour 2023; 8:1220-1223. [PMID: 38188425 PMCID: PMC10769523 DOI: 10.1080/23802359.2023.2275830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/22/2023] [Indexed: 01/09/2024] Open
Abstract
The lowland paca (Cuniculus paca) is a nocturnal, widespread, and solitary large-sized rodent in the family Cuniculidae, and one of the most frequently hunted mammals in the Neotropical forests of Latin America. We assembled the first complete mitochondrial genome of lowland paca using three closely related hystricognath species as reference sequences. The mitochondrial genome is 16,770 basepairs (bp) in length, with similar characteristics of vertebrate mitochondrial genomes. We performed phylogenetic analyses using 26 mitochondrial genome of hystricognath species based on thirteen protein-coding genes. The result confirms the taxonomical placement among the New World hystricognath rodents with high support. The placement is consistent with previous phylogenetic studies based on individual mitochondrial and nuclear genes. The current study improves the phylogenic resolution of hystricognath rodents.
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Affiliation(s)
- Juan Li
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Biologie, Chemie, and Pharmazie, Freie Universität Berlin, Berlin, Germany
| | - Pedro Mayor
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
- ComFauna, Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica, Iquitos, Peru
| | - Meddly L. Santolalla Robles
- School of Public Health and Administration, Emerge, Emerging Diseases and Climate Change Research Unit, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alex D. Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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44
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Bush ZD, Naftaly AFS, Dinwiddie D, Albers C, Hillers KJ, Libuda DE. Comprehensive detection of structural variation and transposable element differences between wild type laboratory lineages of C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523974. [PMID: 37961628 PMCID: PMC10634987 DOI: 10.1101/2023.01.13.523974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Genomic structural variations (SVs) and transposable elements (TEs) can be significant contributors to genome evolution, altered gene expression, and risk of genetic diseases. Recent advancements in long-read sequencing have greatly improved the quality of de novo genome assemblies and enhanced the detection of sequence variants at the scale of hundreds or thousands of bases. Comparisons between two diverged wild isolates of Caenorhabditis elegans, the Bristol and Hawaiian strains, have been widely utilized in the analysis of small genetic variations. Genetic drift, including SVs and rearrangements of repeated sequences such as TEs, can occur over time from long-term maintenance of wild type isolates within the laboratory. To comprehensively detect both large and small structural variations as well as TEs due to genetic drift, we generated de novo genome assemblies and annotations for each strain from our lab collection using both long- and short-read sequencing and compared our assemblies and annotations with that of other lab wild type strains. Within our lab assemblies, we annotate over 3.1Mb of sequence divergence between the Bristol and Hawaiian isolates: 337,584 SNPs, 94,503 small insertion-deletions (<50bp), and 4,334 structural variations (>50bp). Further, we define the location and movement of specific DNA TEs between N2 Bristol and CB4856 Hawaiian wild type isolates. Specifically, we find the N2 Bristol genome has 20.6% more TEs from the Tc1/mariner family than the CB4856 Hawaiian genome. Moreover, we identified Zator elements as the most abundant and mobile TE family in the genome. Using specific TE sequences with unique SNPs, we also identify 38 TEs that moved intrachromosomally and 9 TEs that moved interchromosomally between the N2 Bristol and CB4856 Hawaiian genomes. By comparing the de novo genome assembly of our lab collection Bristol isolate to the VC2010 Bristol assembly, we also reveal that lab lineages display over 2 Mb of total variation: 1,162 SNPs, 1,528 indels, and 897 SVs with 95% of the variation due to SVs. Overall, our work demonstrates the unique contribution of SVs and TEs to variation and genetic drift between wild type laboratory strains assumed to be isogenic despite growing evidence of genetic drift and phenotypic variation.
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Affiliation(s)
- Zachary D. Bush
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Alice F. S. Naftaly
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Devin Dinwiddie
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Cora Albers
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Kenneth J. Hillers
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
| | - Diana E. Libuda
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
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45
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Dey R, Alshaweesh J, Singh KP, Lypaczewski P, Karmakar S, Klenow L, Paulini K, Kaviraj S, Kamhawi S, Valenzuela JG, Singh S, Hamano S, Satoskar AR, Gannavaram S, Nakhasi HL, Matlashewski G. Production of leishmanin skin test antigen from Leishmania donovani for future reintroduction in the field. Nat Commun 2023; 14:7028. [PMID: 37919280 PMCID: PMC10622560 DOI: 10.1038/s41467-023-42732-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023] Open
Abstract
The leishmanin skin test was used for almost a century to detect exposure and immunity to Leishmania, the causative agent of leishmaniasis, a major neglected tropical disease. Due to a lack of antigen used for the intradermal injection, the leishmanin skin test is no longer available. As leishmaniasis control programs are advancing and new vaccines are entering clinical trials, it is essential to re-introduce the leishmanin skin test. Here we establish a Leishmania donovani strain and describe the production, under Good Laboratory Practice conditions, of leishmanin soluble antigen used to induce the leishmanin skin test in animal models of infection and vaccination. Using a mouse model of cutaneous leishmaniasis and a hamster model of visceral leishmaniasis, soluble antigen induces a leishmanin skin test response following infection and vaccination with live attenuated Leishmania major (LmCen-/-). Both the CD4+ and CD8+ T-cells are necessary for the leishmanin skin test response. This study demonstrates the feasibility of large-scale production of leishmanin antigen addressing a major bottleneck for performing the leishmanin skin test in future surveillance and vaccine clinical trials.
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Affiliation(s)
- Ranadhir Dey
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA
| | - Jalal Alshaweesh
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- The Joint Usage/Research Center on Tropical Disease, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | | | - Patrick Lypaczewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Subir Karmakar
- Gennova Biopharmaceuticals, Hinjawadi Phase II, Pune, Maharashtra, India
| | - Laura Klenow
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA
| | - Kayla Paulini
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Swarnendu Kaviraj
- Gennova Biopharmaceuticals, Hinjawadi Phase II, Pune, Maharashtra, India
| | - Shaden Kamhawi
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland, 20852, USA
| | - Jesus G Valenzuela
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland, 20852, USA
| | - Sanjay Singh
- Gennova Biopharmaceuticals, Hinjawadi Phase II, Pune, Maharashtra, India.
| | - Shinjiro Hamano
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.
- The Joint Usage/Research Center on Tropical Disease, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.
| | - Abhay R Satoskar
- Department of Pathology and Microbiology, Ohio State University, Columbus, OH, USA.
| | - Sreenivas Gannavaram
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA.
| | - Hira L Nakhasi
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA.
| | - Greg Matlashewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
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46
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Yuan R, Li J, Ma X, Feng Z, Xing R, Chen S, Gao Q. Investigation of phylogenetic relationships within Saxifraga diversifolia complex (Saxifragaceae) based on restriction-site associated DNA sequence markers. Ecol Evol 2023; 13:e10675. [PMID: 37928197 PMCID: PMC10620575 DOI: 10.1002/ece3.10675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023] Open
Abstract
Subsect. Hirculoideae Engl. & Irmsch., belonging to Saxifraga sect. Ciliatae Haw., has high species richness. It can be divided into S. diversifolia, S. pseudohirculus, and S. sinomontana complexes based on morphological characteristics. The species with prominent leaf veins on the posterior leaf edge were placed in the S. diversifolia complex, which is mainly distributed on the eastern and southern margins of the Qinghai-Tibetan Plateau. In this study, 53 samples, representing 15 of the 33 described species in the S. diversifolia complex, were sequenced using the Restriction-site Associated DNA Sequence (RAD-seq) technique. A total of 111,938 high-quality SNP loci were screened to investigate the phylogenetic relationships within the S. diversifolia complex. The result of the neighbor-joining (NJ) tree shows that the S. diversifolia complex is a paraphyletic group. Despite of some inconsistencies as revealed by genetic structural analysis, clustering results of representative species reconstructed by both NJ and principal component analysis analyses support previous biogeographic and morphological evidences. In addition, long-distance gene flow events for 11 taxa were detected in the S. diversifolia complex, respectively from S. implicans 1 to S. implicans 2, S. diversifolia and S. maxionggouensis, and from S. maxionggouensis to S. nigroglandulifera. These findings may improve our comprehension of the phylogeny, classification, and evolution of the S. diversifolia complex.
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Affiliation(s)
- Rui Yuan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Jiaxin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Xiaolei Ma
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Zhilin Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Rui Xing
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology Chinese Academy of Sciences Xining China
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47
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Zhang S, Yang W, Chen J, Zhang C, Zhang S, Gao L. Whole genome sequencing and annotation of Scleroderma yunnanense, the only edible Scleroderma species. Genomics 2023; 115:110727. [PMID: 37839651 DOI: 10.1016/j.ygeno.2023.110727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/18/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
Scleroderma yunnanense, an ectomycorrhizal fungus, is a popular edible mushroom within the Yunnan Province of Southwest China that holds great ecological and economic implications. However, despite its significance, there remains limited information about this species. Therefore, we sequenced S. yunnanense genome to identify the functional genes of S. yunnanense involved in secondary metabolite and carbohydrate production pathways. First, we present the 40.43 Mb high-quality reference genome for S. yunnanense, distributed across 35 contigs; moreover, the N50 contig size was found to reach 3.31 Mb and contained 8877 functional genes. Finally, genome annotation was conducted to compare the functional genes of S. yunnanense with protein sequences from different publicly available databases. Taken together, we identified 12 biosynthetic gene clusters across 10 contigs; among these were 13 key mevalonate (MVA) pathway enzymes, a key tyrosinase enzyme in the 3,4-dihydroxyphenylalanine (DOPA) pathway that is responsible for producing DOPA melanins, and 16 enzymes involved in uridine diphosphate glucose biosynthesis. Overall, this study presents the first genome assembly and annotation of S. yunnanense; ultimately, this information will be important in the elucidation of the biological activities and artificial domestication of this fungus.
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Affiliation(s)
- Shanshan Zhang
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Wenzhong Yang
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Jian Chen
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Chuanguang Zhang
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Siqi Zhang
- Wenshan Prefecture Central Blood Station, Yunnan 663099, China
| | - Lanjing Gao
- College of Forestry, Beijing Forestry University, Beijing 100083, China
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48
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Mack KL, Talbott HE, Griffin MF, Parker JBL, Guardino NJ, Spielman AF, Davitt MF, Mascharak S, Downer M, Morgan A, Valencia C, Akras D, Berger MJ, Wan DC, Fraser HB, Longaker MT. Allele-specific expression reveals genetic drivers of tissue regeneration in mice. Cell Stem Cell 2023; 30:1368-1381.e6. [PMID: 37714154 PMCID: PMC10592051 DOI: 10.1016/j.stem.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 06/16/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
In adult mammals, skin wounds typically heal by scarring rather than through regeneration. In contrast, "super-healer" Murphy Roths Large (MRL) mice have the unusual ability to regenerate ear punch wounds; however, the molecular basis for this regeneration remains elusive. Here, in hybrid crosses between MRL and non-regenerating mice, we used allele-specific gene expression to identify cis-regulatory variation associated with ear regeneration. Analyzing three major cell populations (immune, fibroblast, and endothelial), we found that genes with cis-regulatory differences specifically in fibroblasts were associated with wound-healing pathways and also co-localized with quantitative trait loci for ear wound-healing. Ectopic treatment with one of these proteins, complement factor H (CFH), accelerated wound repair and induced regeneration in typically fibrotic wounds. Through single-cell RNA sequencing (RNA-seq), we observed that CFH treatment dramatically reduced immune cell recruitment to wounds, suggesting a potential mechanism for CFH's effect. Overall, our results provide insights into the molecular drivers of regeneration with potential clinical implications.
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Affiliation(s)
- Katya L Mack
- Stanford University, Department of Biology, Stanford, CA, USA
| | - Heather E Talbott
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA
| | - Michelle F Griffin
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Jennifer B L Parker
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA
| | - Nicholas J Guardino
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Amanda F Spielman
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Michael F Davitt
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Shamik Mascharak
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA
| | - Mauricio Downer
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Annah Morgan
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Caleb Valencia
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Deena Akras
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Mark J Berger
- Stanford University, Department of Computer Science, Stanford, CA 94305, USA
| | - Derrick C Wan
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Hunter B Fraser
- Stanford University, Department of Biology, Stanford, CA, USA.
| | - Michael T Longaker
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA.
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49
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Agustí C, Martínez-Riveros H, Hernández-Rodríguez À, Casañ C, Díaz Y, Alonso L, Martró E, Muñoz-Basagoiti J, Gallemí M, Folch C, Sönmez I, Adell H, Villar M, París de León A, Martinez-Puchol S, Pelegrin AC, Perez-Zsolt D, Raïch-Regué D, Mora R, Villegas L, Clotet B, Izquierdo-Useros N, Cardona PJ, Casabona J. Self-sampling monkeypox virus testing in high-risk populations, asymptomatic or with unrecognized Mpox, in Spain. Nat Commun 2023; 14:5998. [PMID: 37783731 PMCID: PMC10545734 DOI: 10.1038/s41467-023-40490-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/31/2023] [Indexed: 10/04/2023] Open
Abstract
The recent monkeypox virus (MPXV) outbreak was of global concern and has mainly affected gay, bisexual and other men who have sex with men (GBMSM). Here we assess prevalence of MPXV in high-risk populations of GBMSM, trans women (TW) and non-binary people without symptoms or with unrecognized monkeypox (Mpox) symptoms, using a self-sampling strategy. Anal and pharyngeal swabs are tested by MPXV real-time PCR and positive samples are tested for cytopathic effect (CPE) in cell culture. 113 individuals participated in the study, 89 (78.76%) were cis men, 17 (15.04%) were TW. The median age was 35.0 years (IQR: 30.0-43.0), 96 (85.02%) individuals were gay or bisexual and 72 (63.72%) were migrants. Seven participants were MPXV positive (6.19% (95% CI: 1.75%-10.64%)). Five tested positive in pharyngeal swabs, one in anal swab and one in both. Six did not present symptoms recognized as MPXV infection. Three samples were positive for CPE, and showed anti-vaccinia pAb staining by FACS and confocal microscopy. This suggests that unrecognized Mpox cases can shed infectious virus. Restricting testing to individuals reporting Mpox symptoms may not be sufficient to contain outbreaks.
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Affiliation(s)
- Cristina Agustí
- Centre of epidemiological studies on sexually transmitted infections and AIDS of Catalunya (CEEISCAT), Department of Health, Government of Catalonia, Badalona, Spain.
- Biomedical Research Center Network for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain.
| | - Héctor Martínez-Riveros
- Centre of epidemiological studies on sexually transmitted infections and AIDS of Catalunya (CEEISCAT), Department of Health, Government of Catalonia, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- Doctorate Program in Methodology of Biomedical Research and Public Health, Department of Paediatrics, Obstetrics and Gynaecology and Preventive Medicine, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Àgueda Hernández-Rodríguez
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Germans Trias i Pujol University Hospital, Badalona, Spain
- Departament of Genetics and Microbiology, Autonomous University of Barcelona, Badalona, Spain
| | - Cristina Casañ
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Yesika Díaz
- Centre of epidemiological studies on sexually transmitted infections and AIDS of Catalunya (CEEISCAT), Department of Health, Government of Catalonia, Badalona, Spain
| | - Lucía Alonso
- Centre of epidemiological studies on sexually transmitted infections and AIDS of Catalunya (CEEISCAT), Department of Health, Government of Catalonia, Badalona, Spain
- Fundació Lluita contra las Infeccions, Infectious Diseases Department, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Elisa Martró
- Biomedical Research Center Network for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Germans Trias i Pujol University Hospital, Badalona, Spain
- Departament of Genetics and Microbiology, Autonomous University of Barcelona, Badalona, Spain
| | | | - Marçal Gallemí
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Cinta Folch
- Centre of epidemiological studies on sexually transmitted infections and AIDS of Catalunya (CEEISCAT), Department of Health, Government of Catalonia, Badalona, Spain
- Biomedical Research Center Network for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
| | - Ibrahim Sönmez
- Centre of epidemiological studies on sexually transmitted infections and AIDS of Catalunya (CEEISCAT), Department of Health, Government of Catalonia, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
| | | | | | - Alexia París de León
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Sandra Martinez-Puchol
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Germans Trias i Pujol University Hospital, Badalona, Spain
- Vicerectorat de Recerca, Universitat de Barcelona, Universitat de Barcelona(UB), Barcelona, Spain
| | - A C Pelegrin
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Daniel Perez-Zsolt
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Dàlia Raïch-Regué
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | | | | | - Bonaventura Clotet
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- Fundació Lluita contra las Infeccions, Infectious Diseases Department, Hospital Germans Trias i Pujol, Badalona, Spain
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- University of Vic-Central University of Catalonia (uVic-UCC), Vic, Spain
- Biomedical Research Center Network for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Nuria Izquierdo-Useros
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
- Biomedical Research Center Network for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Pere-Joan Cardona
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Germans Trias i Pujol University Hospital, Badalona, Spain
- Departament of Genetics and Microbiology, Autonomous University of Barcelona, Badalona, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Casabona
- Centre of epidemiological studies on sexually transmitted infections and AIDS of Catalunya (CEEISCAT), Department of Health, Government of Catalonia, Badalona, Spain
- Biomedical Research Center Network for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- Departament of Genetics and Microbiology, Autonomous University of Barcelona, Badalona, Spain
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50
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Kashima Y, Mizutani T, Okimoto Y, Maeda M, Musashino K, Nishide RI, Matsukura A, Nagase J, Suzuki Y. Evolution of the viral genomes of SARS-CoV-2 in association with the changes in local condition: a genomic epidemiological study of a suburban city of Japan. DNA Res 2023; 30:dsad020. [PMID: 37712596 PMCID: PMC10562954 DOI: 10.1093/dnares/dsad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023] Open
Abstract
Understanding the factors driving the spread and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the local, regional, national, and international levels is important in protecting against future pandemics. By exploring their viral genomes, we attempted to analyse the spread of SARS-CoV-2 and its evolutionary convergence in Kashiwa City, as an example of a representative commuter town in Japan. From September 2020 to January 2023, a total of 47,134 nasopharyngeal swab and saliva specimens were collected from patients in 47 local clinics and hospitals, covering the vast majority of healthcare facilities. All SARS-CoV-2-positive samples were subjected to whole genome sequencing. Based on the analysis of 5,536 identified genomes, all major strains were represented. Unique regional mutations were occasionally identified in each strain. Inspection of these mutations revealed that the overall base substitution rate increased with progressive waves of the pandemic, at an overall rate of 2.56 bases/year. Interestingly, the spread and evolutionary patterns appeared to be distinct between regions and between individual clinics. Further analysis of the synonymous base substitution rate showed that the speed of viral evolution accelerated coincident with the beginning of public vaccination. Comprehensive genomic epidemiological studies, as presented here, should be useful in precisely understanding the pandemic and preparing for possible future pandemics.
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Affiliation(s)
- Yukie Kashima
- Laboratory of Functional Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Taketoshi Mizutani
- Laboratory of Functional Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yuki Okimoto
- Kashiwa City Public Health Center, Kashiwa City, Chiba, Japan
| | - Minami Maeda
- Alluminox and Corporate Development, Rakuten Medical K.K., Tokyo, Japan
| | | | | | | | | | - Yutaka Suzuki
- Laboratory of Functional Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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