151
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Melton AE, Child AW, Beard RS, Dumaguit CDC, Forbey JS, Germino M, de Graaff MA, Kliskey A, Leitch IJ, Martinez P, Novak SJ, Pellicer J, Richardson BA, Self D, Serpe M, Buerki S. A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands. G3 (BETHESDA, MD.) 2022; 12:6585877. [PMID: 35567476 PMCID: PMC9258541 DOI: 10.1093/g3journal/jkac122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022]
Abstract
Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.
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Affiliation(s)
- Anthony E Melton
- Corresponding author: Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
| | | | - Richard S Beard
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | | | - Jennifer S Forbey
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Matthew Germino
- Forest and Rangeland Ecosystem Science Center, United States Geological Survey, Boise, ID 83706, USA
| | | | | | | | - Peggy Martinez
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Stephen J Novak
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Jaume Pellicer
- Royal Botanic Gardens, Richmond TW9 3AE, UK,Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona 08038, Spain
| | - Bryce A Richardson
- Rocky Mountain Research Station, United States Forest Service, Moscow, ID 83843, USA
| | - Desiree Self
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Marcelo Serpe
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Sven Buerki
- Corresponding author: Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
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152
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Wei KHC, Mai D, Chatla K, Bachtrog D. Dynamics and Impacts of Transposable Element Proliferation in the Drosophila nasuta Species Group Radiation. Mol Biol Evol 2022; 39:msac080. [PMID: 35485457 PMCID: PMC9075770 DOI: 10.1093/molbev/msac080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transposable element (TE) mobilization is a constant threat to genome integrity. Eukaryotic organisms have evolved robust defensive mechanisms to suppress their activity, yet TEs can escape suppression and proliferate, creating strong selective pressure for host defense to adapt. This genomic conflict fuels a never-ending arms race that drives the rapid evolution of TEs and recurrent positive selection of genes involved in host defense; the latter has been shown to contribute to postzygotic hybrid incompatibility. However, how TE proliferation impacts genome and regulatory divergence remains poorly understood. Here, we report the highly complete and contiguous (N50 = 33.8-38.0 Mb) genome assemblies of seven closely related Drosophila species that belong to the nasuta species group-a poorly studied group of flies that radiated in the last 2 My. We constructed a high-quality de novo TE library and gathered germline RNA-seq data, which allowed us to comprehensively annotate and compare TE insertion patterns between the species, and infer the evolutionary forces controlling their spread. We find a strong negative association between TE insertion frequency and expression of genes nearby; this likely reflects survivor bias from reduced fitness impact of TEs inserting near lowly expressed, nonessential genes, with limited TE-induced epigenetic silencing. Phylogenetic analyses of insertions of 147 TE families reveal that 53% of them show recent amplification in at least one species. The most highly amplified TE is a nonautonomous DNA element (Drosophila INterspersed Element; DINE) which has gone through multiple bouts of expansions with thousands of full-length copies littered throughout each genome. Across all TEs, we find that TEs expansions are significantly associated with high expression in the expanded species consistent with suppression escape. Thus, whereas horizontal transfer followed by the invasion of a naïve genome has been highlighted to explain the long-term survival of TEs, our analysis suggests that evasion of host suppression of resident TEs is a major strategy to persist over evolutionary times. Altogether, our results shed light on the heterogenous and context-dependent nature in which TEs affect gene regulation and the dynamics of rampant TE proliferation amidst a recently radiated species group.
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Affiliation(s)
- Kevin H.-C. Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dat Mai
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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153
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Nunn A, Rodríguez‐Arévalo I, Tandukar Z, Frels K, Contreras‐Garrido A, Carbonell‐Bejerano P, Zhang P, Ramos Cruz D, Jandrasits K, Lanz C, Brusa A, Mirouze M, Dorn K, Galbraith DW, Jarvis BA, Sedbrook JC, Wyse DL, Otto C, Langenberger D, Stadler PF, Weigel D, Marks MD, Anderson JA, Becker C, Chopra R. Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:944-963. [PMID: 34990041 PMCID: PMC9055812 DOI: 10.1111/pbi.13775] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/28/2021] [Accepted: 12/23/2021] [Indexed: 05/20/2023]
Abstract
Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
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Affiliation(s)
- Adam Nunn
- ecSeq Bioinformatics GmbHLeipzigGermany
- Department of Computer ScienceLeipzig UniversityLeipzigGermany
| | - Isaac Rodríguez‐Arévalo
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Zenith Tandukar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Katherine Frels
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
| | | | | | - Panpan Zhang
- Institut de Recherche pour le DéveloppementUMR232 DIADEMontpellierFrance
- Laboratory of Plant Genome and DevelopmentUniversity of PerpignanPerpignanFrance
| | - Daniela Ramos Cruz
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Katharina Jandrasits
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Christa Lanz
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Anthony Brusa
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Marie Mirouze
- Institut de Recherche pour le DéveloppementUMR232 DIADEMontpellierFrance
- Laboratory of Plant Genome and DevelopmentUniversity of PerpignanPerpignanFrance
| | - Kevin Dorn
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
- USDA‐ARSSoil Management and Sugarbeet ResearchFort CollinsCOUSA
| | - David W Galbraith
- BIO5 InstituteArizona Cancer CenterDepartment of Biomedical EngineeringUniversity of ArizonaSchool of Plant SciencesTucsonAZUSA
| | - Brice A. Jarvis
- School of Biological SciencesIllinois State UniversityNormalILUSA
| | - John C. Sedbrook
- School of Biological SciencesIllinois State UniversityNormalILUSA
| | - Donald L. Wyse
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | | | | | - Peter F. Stadler
- Department of Computer ScienceLeipzig UniversityLeipzigGermany
- Max Planck Institute for Mathematics in the SciencesLeipzigGermany
| | - Detlef Weigel
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - M. David Marks
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
| | - James A. Anderson
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Claude Becker
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Ratan Chopra
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
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154
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Thompson AW, Wojtas H, Davoll M, Braasch I. Genome of the Rio Pearlfish (Nematolebias whitei), a bi-annual killifish model for Eco-Evo-Devo in extreme environments. G3 (BETHESDA, MD.) 2022; 12:6533448. [PMID: 35188191 PMCID: PMC8982402 DOI: 10.1093/g3journal/jkac045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022]
Abstract
The Rio Pearlfish, Nematolebias whitei, is a bi-annual killifish species inhabiting seasonal pools in the Rio de Janeiro region of Brazil that dry twice per year. Embryos enter dormant diapause stages in the soil, waiting for the inundation of the habitat which triggers hatching and commencement of a new life cycle. Rio Pearlfish represents a convergent, independent origin of annualism from other emerging killifish model species. While some transcriptomic datasets are available for Rio Pearlfish, thus far, a sequenced genome has been unavailable. Here, we present a high quality, 1.2 Gb chromosome-level genome assembly, genome annotations, and a comparative genomic investigation of the Rio Pearlfish as representative of a vertebrate clade that evolved environmentally cued hatching. We show conservation of 3D genome structure across teleost fish evolution, developmental stages, tissues, and cell types. Our analysis of mobile DNA shows that Rio Pearlfish, like other annual killifishes, possesses an expanded transposable element profile with implications for rapid aging and adaptation to harsh conditions. We use the Rio Pearlfish genome to identify its hatching enzyme gene repertoire and the location of the hatching gland, a key first step in understanding the developmental genetic control of hatching. The Rio Pearlfish genome expands the comparative genomic toolkit available to study convergent origins of seasonal life histories, diapause, and rapid aging phenotypes. We present the first set of genomic resources for this emerging model organism, critical for future functional genetic, and multiomic explorations of “Eco-Evo-Devo” phenotypes of resilience and adaptation to extreme environments.
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Affiliation(s)
- Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution & Behavior (EEB) Program, Michigan State University, East Lansing, MI 48824, USA
| | - Harrison Wojtas
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Myles Davoll
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution & Behavior (EEB) Program, Michigan State University, East Lansing, MI 48824, USA
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155
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Huerlimann R, Cowley JA, Wade NM, Wang Y, Kasinadhuni N, Chan CKK, Jabbari JS, Siemering K, Gordon L, Tinning M, Montenegro JD, Maes GE, Sellars MJ, Coman GJ, McWilliam S, Zenger KR, Khatkar MS, Raadsma HW, Donovan D, Krishna G, Jerry DR. Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence. G3 (BETHESDA, MD.) 2022; 12:6526390. [PMID: 35143647 PMCID: PMC8982415 DOI: 10.1093/g3journal/jkac034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/02/2022] [Indexed: 01/08/2023]
Abstract
Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.
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Affiliation(s)
- Roger Huerlimann
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Jeff A Cowley
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Nicholas M Wade
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Yinan Wang
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Naga Kasinadhuni
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Chon-Kit Kenneth Chan
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Jafar S Jabbari
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Kirby Siemering
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Lavinia Gordon
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Matthew Tinning
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Juan D Montenegro
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia.,Laboratory of Biodiversity and Evolutionary Genomics, Biogenomics-consultancy, KU Leuven, Leuven 3000, Belgium.,Center for Human Genetics, UZ Leuven- Genomics Core, KU Leuven, Leuven 3000, Belgium
| | | | - Greg J Coman
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,CSIRO Agriculture and Food, Bribie Island Research Centre, Woorim, QLD 4507, Australia
| | - Sean McWilliam
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Kyall R Zenger
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Mehar S Khatkar
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Herman W Raadsma
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Dallas Donovan
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Seafarms Group Ltd, Darwin, NT 0800, Australia
| | - Gopala Krishna
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Seafarms Group Ltd, Darwin, NT 0800, Australia
| | - Dean R Jerry
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
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156
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Zwyrtková J, Blavet N, Doležalová A, Cápal P, Said M, Molnár I, Vrána J, Doležel J, Hřibová E. Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers. Int J Mol Sci 2022; 23:ijms23063191. [PMID: 35328613 PMCID: PMC8948999 DOI: 10.3390/ijms23063191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 02/01/2023] Open
Abstract
Crested wheatgrass (Agropyron cristatum), a wild relative of wheat, is an attractive source of genes and alleles for their improvement. Its wider use is hampered by limited knowledge of its complex genome. In this work, individual chromosomes were purified by flow sorting, and DNA shotgun sequencing was performed. The annotation of chromosome-specific sequences characterized the DNA-repeat content and led to the identification of genic sequences. Among them, genic sequences homologous to genes conferring plant disease resistance and involved in plant tolerance to biotic and abiotic stress were identified. Genes belonging to the important groups for breeders involved in different functional categories were found. The analysis of the DNA-repeat content identified a new LTR element, Agrocen, which is enriched in centromeric regions. The colocalization of the element with the centromeric histone H3 variant CENH3 suggested its functional role in the grass centromere. Finally, 159 polymorphic simple-sequence-repeat (SSR) markers were identified, with 72 of them being chromosome- or chromosome-arm-specific, 16 mapping to more than one chromosome, and 71 mapping to all the Agropyron chromosomes. The markers were used to characterize orthologous relationships between A. cristatum and common wheat that will facilitate the introgression breeding of wheat using A. cristatum.
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157
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Yu C, Diao Y, Lu Q, Zhao J, Cui S, Xiong X, Lu A, Zhang X, Liu H. Comparative Genomics Reveals Evolutionary Traits, Mating Strategies, and Pathogenicity-Related Genes Variation of Botryosphaeriaceae. Front Microbiol 2022; 13:800981. [PMID: 35283828 PMCID: PMC8905617 DOI: 10.3389/fmicb.2022.800981] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Botryosphaeriaceae, as a major family of the largest class of kingdom fungi Dothideomycetes, encompasses phytopathogens, saprobes, and endophytes. Many members of this family are opportunistic phytopathogens with a wide host range and worldwide geographical distribution, and can infect many economically important plants, including food crops and raw material plants for biofuel production. To date, however, little is known about the family evolutionary characterization, mating strategies, and pathogenicity-related genes variation from a comparative genome perspective. Here, we conducted a large-scale whole-genome comparison of 271 Dothideomycetes, including 19 species in Botryosphaeriaceae. The comparative genome analysis provided a clear classification of Botryosphaeriaceae in Dothideomycetes and indicated that the evolution of lifestyle within Dothideomycetes underwent four major transitions from non-phytopathogenic to phytopathogenic. Mating strategies analysis demonstrated that at least 3 transitions were found within Botryosphaeriaceae from heterothallism to homothallism. Additionally, pathogenicity-related genes contents in different genera varied greatly, indicative of genus-lineage expansion within Botryosphaeriaceae. These findings shed new light on evolutionary traits, mating strategies and pathogenicity-related genes variation of Botryosphaeriaceae.
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Affiliation(s)
- Chengming Yu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Yufei Diao
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Quan Lu
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Jiaping Zhao
- Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, China
| | - Shengnan Cui
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Xiong Xiong
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Anna Lu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Xingyao Zhang
- Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, China
| | - Huixiang Liu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
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158
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Bae EK, An C, Kang MJ, Lee SA, Lee SJ, Kim KT, Park EJ. Chromosome-level genome assembly of the fully mycoheterotrophic orchid Gastrodia elata. G3 (BETHESDA, MD.) 2022; 12:6511440. [PMID: 35100375 PMCID: PMC8896018 DOI: 10.1093/g3journal/jkab433] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/10/2021] [Indexed: 11/26/2022]
Abstract
Gastrodia elata, an obligate mycoheterotrophic orchid, requires complete carbon and mineral nutrient supplementation from mycorrhizal fungi during its entire life cycle. Although full mycoheterotrophy occurs most often in the Orchidaceae family, no chromosome-level reference genome from this group has been assembled to date. Here, we report a high-quality chromosome-level genome assembly of G. elata, using Illumina and PacBio sequencing methods with Hi-C technique. The assembled genome size was found to be 1045 Mb, with an N50 of 50.6 Mb and 488 scaffolds. A total of 935 complete (64.9%) matches to the 1440 embryophyte Benchmarking Universal Single-Copy Orthologs were identified in this genome assembly. Hi-C scaffolding of the assembled genome resulted in 18 pseudochromosomes, 1008 Mb in size and containing 96.5% of the scaffolds. A total of 18,844 protein-coding sequences (CDSs) were predicted in the G. elata genome, of which 15,619 CDSs (82.89%) were functionally annotated. In addition, 74.92% of the assembled genome was found to be composed of transposable elements. Phylogenetic analysis indicated a significant contraction of genes involved in various biosynthetic processes and cellular components and an expansion of genes for novel metabolic processes and mycorrhizal association. This result suggests an evolutionary adaptation of G. elata to a mycoheterotrophic lifestyle. In summary, the genomic resources generated in this study will provide a valuable reference genome for investigating the molecular mechanisms of G. elata biological functions. Furthermore, the complete G. elata genome will greatly improve our understanding of the genetics of Orchidaceae and its mycoheterotrophic evolution.
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Affiliation(s)
- Eun-Kyung Bae
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
| | - Chanhoon An
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
| | - Min-Jeong Kang
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
| | - Sang-A Lee
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
| | - Seung Jae Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon 57922, Korea
| | - Eung-Jun Park
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
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159
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Li X, Cai K, Han Z, Zhang S, Sun A, Xie Y, Han R, Guo R, Tigabu M, Sederoff R, Pei X, Zhao C, Zhao X. Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change. FRONTIERS IN PLANT SCIENCE 2022; 13:850054. [PMID: 35310631 PMCID: PMC8927880 DOI: 10.3389/fpls.2022.850054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Acer pseudosieboldianum (Pax) Komarov is an ornamental plant with prominent potential and is naturally distributed in Northeast China. Here, we obtained a chromosome-scale genome assembly of A. pseudosieboldianum combining HiFi and Hi-C data, and the final assembled genome size was 690.24 Mb and consisted of 287 contigs, with a contig N50 value of 5.7 Mb and a BUSCO complete gene percentage of 98.4%. Genome evolution analysis showed that an ancient duplication occurred in A. pseudosieboldianum. Phylogenetic analyses revealed that Aceraceae family could be incorporated into Sapindaceae, consistent with the present Angiosperm Phylogeny Group system. We further construct a gene-to-metabolite correlation network and identified key genes and metabolites that might be involved in anthocyanin biosynthesis pathways during leaf color change. Additionally, we identified crucial teosinte branched1, cycloidea, and proliferating cell factors (TCP) transcription factors that might be involved in leaf morphology regulation of A. pseudosieboldianum, Acer yangbiense and Acer truncatum. Overall, this reference genome is a valuable resource for evolutionary history studies of A. pseudosieboldianum and lays a fundamental foundation for its molecular breeding.
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Affiliation(s)
- Xiang Li
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Kewei Cai
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Zhiming Han
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Shikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Anran Sun
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Ying Xie
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
| | - Rui Han
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Ruixue Guo
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Mulualem Tigabu
- Southern Swedish Forest Research Centre, Faculty of Forest Science, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Xiaona Pei
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Chunli Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Xiyang Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, China
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160
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Meng Y, Liang Y, Liao B, He W, Liu Q, Shen X, Xu J, Chen S. Genome-Wide Identification, Characterization and Expression Analysis of Lipoxygenase Gene Family in Artemisia annua L. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050655. [PMID: 35270126 PMCID: PMC8912875 DOI: 10.3390/plants11050655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 05/17/2023]
Abstract
Lipoxygenase (LOX) is a ubiquitous oxygenase found in animals and plants and plays a pivotal role in diverse biological processes, including defense and development. Artemisinin, which can only be obtained from Artemisia annua L., is the most effective therapeutic drug for malaria without serious side effects. This study identified and analyzed LOX gene family members in the A. annua genome at the chromosomal level. Twenty LOX genes with various molecular weights, isoelectric points, and amino acid numbers were identified and named AaLOX, which were located in the cytoplasm or chloroplast. The average protein length of all AaLOX was 850 aa. Phylogenetic tree analysis revealed that the AaLOX was divided into two major groups, 9-LOX and 13-LOX. The exon numbers ranged from 1 to 12, indicating that different AaLOX genes have different functions. The secondary structure was mainly composed of alpha helix and random coil, and the tertiary structure was similar for most AaLOX. Upstream promoter region analysis revealed that a large number of cis-acting elements were closely related to plant growth and development, light response, hormone, and other stress responses. Transcriptome data analysis of different tissues suggested that the gene family was differently expressed in the roots, stems, leaves, and flowers of two A. annua strains HAN1 and LQ9. qRT-PCR confirmed that AaLOX5 and AaLOX17 had the highest expression in flowers and leaves. This study provides a theoretical basis for the further functional analysis of the AaLOX gene family.
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Affiliation(s)
- Ying Meng
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250000, China;
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Yu Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
- College of Pharmaceutical Science, Dali University, Dali 671000, China;
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Wenrui He
- College of Pharmaceutical Science, Dali University, Dali 671000, China;
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610000, China
| | - Qianwen Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Xiaofeng Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
- Correspondence: (J.X.); (S.C.)
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
- Correspondence: (J.X.); (S.C.)
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161
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int J Mol Sci 2022; 23:2671. [PMID: 35269811 PMCID: PMC8910360 DOI: 10.3390/ijms23052671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (C.G.T.F.); (B.J.N.); (M.F.D.); (M.G.); (J.P.); (P.E.B.); (P.M.F.); (J.B.)
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162
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Jaron KS, Parker DJ, Anselmetti Y, Tran Van P, Bast J, Dumas Z, Figuet E, François CM, Hayward K, Rossier V, Simion P, Robinson-Rechavi M, Galtier N, Schwander T. Convergent consequences of parthenogenesis on stick insect genomes. SCIENCE ADVANCES 2022; 8:eabg3842. [PMID: 35196080 PMCID: PMC8865771 DOI: 10.1126/sciadv.abg3842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generated reference genomes for five independently evolved parthenogenetic species in the stick insect genus Timema and their closest sexual relatives. Using these references and population genomic data, we show that parthenogenesis results in an extreme reduction of heterozygosity and often leads to genetically uniform populations. We also find evidence for less effective positive selection in parthenogenetic species, suggesting that sex is ubiquitous in natural populations because it facilitates fast rates of adaptation. Parthenogenetic species did not show increased transposable element (TE) accumulation, likely because there is little TE activity in the genus. By using replicated sexual-parthenogenetic comparisons, our study reveals how the absence of sex affects genome evolution in natural populations, providing empirical support for the negative consequences of parthenogenesis as predicted by theory.
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Affiliation(s)
- Kamil S. Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | - Darren J. Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | | | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emeric Figuet
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | | | - Keith Hayward
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Victor Rossier
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Simion
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Galtier
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
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163
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Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings. Proc Natl Acad Sci U S A 2022; 119:2108661119. [PMID: 35169073 PMCID: PMC8872758 DOI: 10.1073/pnas.2108661119] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Where do butterfly eyespots come from? One of the long-standing questions in the field of evolution concerns addressing where novel complex traits come from. Here we show that butterfly eyespots, a novel complex trait, likely originated from the redeployment of a preexisting gene-regulatory network regulating antennae, legs, and wings, to novel locations on the wing. Butterfly eyespots are beautiful novel traits with an unknown developmental origin. Here we show that eyespots likely originated via cooption of parts of an ancestral appendage gene-regulatory network (GRN) to novel locations on the wing. Using comparative transcriptome analysis, we show that eyespots cluster most closely with antennae, relative to multiple other tissues. Furthermore, three genes essential for eyespot development, Distal-less (Dll), spalt (sal), and Antennapedia (Antp), share similar regulatory connections as those observed in the antennal GRN. CRISPR knockout of cis-regulatory elements (CREs) for Dll and sal led to the loss of eyespots, antennae, legs, and also wings, demonstrating that these CREs are highly pleiotropic. We conclude that eyespots likely reused an ancient GRN for their development, a network also previously implicated in the development of antennae, legs, and wings.
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164
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Defining the caprine γδ T cell WC1 multigenic array and evaluation of its expressed sequences and gene structure conservation among goat breeds and relative to cattle. Immunogenetics 2022; 74:347-365. [PMID: 35138437 DOI: 10.1007/s00251-022-01254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/18/2022] [Indexed: 11/05/2022]
Abstract
Workshop cluster 1 (WC1) molecules are part of the scavenger receptor cysteine-rich (SRCR) superfamily and act as hybrid co-receptors for the γδ T cell receptor and as pattern recognition receptors for binding pathogens. These members of the CD163 gene family are expressed on γδ T cells in the blood of ruminants. While the presence of WC1+ γδ T cells in the blood of goats has been demonstrated using monoclonal antibodies, there was no information available about the goat WC1 gene family. The caprine WC1 multigenic array was characterized here for number, structure and expression of genes, and similarity to WC1 genes of cattle and among goat breeds. We found sequence for 17 complete WC1 genes and evidence for up to 30 SRCR a1 or d1 domains which represent distinct signature domains for individual genes. This suggests substantially more WC1 genes than in cattle. Moreover, goats had seven different WC1 gene structures of which 4 are unique to goats. Caprine WC1 genes also had multiple transcript splice variants of their intracytoplasmic domains that eliminated tyrosines shown previously to be important for signal transduction. The most distal WC1 SRCR a1 domains were highly conserved among goat breeds, but fewer were conserved between goats and cattle. Since goats have a greater number of WC1 genes and unique WC1 gene structures relative to cattle, goat WC1 molecules may have expanded functions. This finding may impact research on next-generation vaccines designed to stimulate γδ T cells.
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165
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Harney E, Paterson S, Collin H, Chan BH, Bennett D, Plaistow SJ. Pollution induces epigenetic effects that are stably transmitted across multiple generations. Evol Lett 2022; 6:118-135. [PMID: 35386832 PMCID: PMC8966472 DOI: 10.1002/evl3.273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
It has been hypothesized that the effects of pollutants on phenotypes can be passed to subsequent generations through epigenetic inheritance, affecting populations long after the removal of a pollutant. But there is still little evidence that pollutants can induce persistent epigenetic effects in animals. Here, we show that low doses of commonly used pollutants induce genome‐wide differences in cytosine methylation in the freshwater crustacean Daphnia pulex. Uniclonal populations were either continually exposed to pollutants or switched to clean water, and methylation was compared to control populations that did not experience pollutant exposure. Although some direct changes to methylation were only present in the continually exposed populations, others were present in both the continually exposed and switched to clean water treatments, suggesting that these modifications had persisted for 7 months (>15 generations). We also identified modifications that were only present in the populations that had switched to clean water, indicating a long‐term legacy of pollutant exposure distinct from the persistent effects. Pollutant‐induced differential methylation tended to occur at sites that were highly methylated in controls. Modifications that were observed in both continually and switched treatments were highly methylated in controls and showed reduced methylation in the treatments. On the other hand, modifications found just in the switched treatment tended to have lower levels of methylation in the controls and showed increase methylation in the switched treatment. In a second experiment, we confirmed that sublethal doses of the same pollutants generate effects on life histories for at least three generations following the removal of the pollutant. Our results demonstrate that even low doses of pollutants can induce transgenerational epigenetic effects that are stably transmitted over many generations. Persistent effects are likely to influence phenotypic development, which could contribute to the rapid adaptation, or extinction, of populations confronted by anthropogenic stressors.
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Affiliation(s)
- Ewan Harney
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
- Current address: Institute of Evolutionary Biology (CSIC‐UPF) CMIMA Building Barcelona 08003 Spain
| | - Steve Paterson
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Hélène Collin
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Brian H.K. Chan
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
- Current address: Faculty of Biology, Medicine and Health The University of Manchester Manchester M13 9PT United Kingdom
| | - Daimark Bennett
- Molecular and Physiology Cell Signalling, Institute of Systems, Molecular and Integrative Biology University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Stewart J. Plaistow
- Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool L69 7ZB United Kingdom
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166
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Al Salameen F, Habibi N, Al Amad S, Al Doaij B. Data on draft genome assembly and annotation of Haloxylon salicornicum Moq. Data Brief 2022; 40:107721. [PMID: 35005129 PMCID: PMC8717446 DOI: 10.1016/j.dib.2021.107721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 11/26/2022] Open
Abstract
Haloxylon salicornicum Moq. Bunge ex Boiss (Rimth) is one of the main structural elements in Eastern Arabian vegetation associations. The plant is utilized as a food source for domestic stock, stabilizes the soil surface besides providing suitable microclimates for exotic species. It is considered one of the most promising species for re-vegetation. H. salicornicum community is under threat from overgrazing leading to a reduction in the percentage of distribution from 22.7% to 2.2% in Kuwait. Therefore, genome characterization of this important Kuwaiti plant is required to formulate strategies for its conservation. Here we report the draft of the H. salicornicum genome, which was sequenced on an Illumina HiSeq 2500 platform. BUSCO assessment revealed 69% of the genome was to be complete. Overall, 12960 gene structures, 11280 protein-coding genes, 11309 mRNAs (protein-coding), 51265 exons and 48100 CDSs were predicted. Functional annotation was carried out by interproscan-5.29-68.0. A total of 7222 protein-coding sequences were, annotated out of 11309 by at least one ontology term. All these genes were associated with 11 major biological processes branched into 60 child processes.
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Affiliation(s)
- Fadila Al Salameen
- Environment and Life Sciences Research Centre, Kuwait Institute for Scientific Research, Kuwait
| | - Nazima Habibi
- Environment and Life Sciences Research Centre, Kuwait Institute for Scientific Research, Kuwait
| | - Sami Al Amad
- Environment and Life Sciences Research Centre, Kuwait Institute for Scientific Research, Kuwait
| | - Bashayer Al Doaij
- Environment and Life Sciences Research Centre, Kuwait Institute for Scientific Research, Kuwait
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167
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Yang S, Coleman JJ, Vinatzer BA. Genome Resource: Draft Genome of Fusarium avenaceum, Strain F156N33, Isolated from the Atmosphere Above Virginia and Annotated Based on RNA Sequencing Data. PLANT DISEASE 2022; 106:720-722. [PMID: 34293917 DOI: 10.1094/pdis-04-21-0787-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fusarium avenaceum is a filamentous fungus commonly associated with plants and soil. It is a causal agent of Fusarium head blight (FHB) on maize and small-grain cereals and blights on other plant species, and is one of the very few fungal species known to have ice nucleation activity (i.e., it catalyzes ice formation). Here, we report the draft genome of the ice-nucleation-active F. avenaceum strain F156N33 isolated from the atmosphere above Virginia. The genome assembly is 41,175,306 bp long, consists of 214 contigs, and is predicted to encode 11,233 proteins, which were annotated using RNA-sequencing data obtained from the same strain.
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Affiliation(s)
- Shu Yang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
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168
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Ambardar S, Vakhlu J, Sowdhamini R. Insights from the analysis of draft genome sequence of Crocus sativus L. Bioinformation 2022; 18:1-13. [PMID: 35815202 PMCID: PMC9200609 DOI: 10.6026/97320630018001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/31/2021] [Accepted: 10/31/2021] [Indexed: 11/23/2022] Open
Abstract
Saffron (Crocus sativus L.) is the low yielding plant of medicinal and economic importance. Therefore, it is of interest to report the draft genome sequence of C. sativus. The draft genome of C. sativus has been assembled using Illumina sequencing and is 3.01 Gb long covering 84.24% of genome. C. sativus genome annotation identified 53,546 functional genes (including 5726 transcription factors), 862,275 repeats and 964,231 SSR markers. The genes involved in the apocarotenoids biosynthesis pathway (crocin, crocetin, picrocrocin, and safranal) were found in the draft genome analysis.
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Affiliation(s)
- Sheetal Ambardar
- National Center for Biological Sciences, Bellary Road, Bengaluru, India
| | - Jyoti Vakhlu
- School of Biotechnology, University of Jammu, J&K, India
| | - Ramanathan Sowdhamini
- National Center for Biological Sciences, Bellary Road, Bengaluru, India
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, India
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169
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Tomé LMR, da Silva FF, Fonseca PLC, Mendes-Pereira T, Azevedo VADC, Brenig B, Badotti F, Góes-Neto A. Hybrid Assembly Improves Genome Quality and Completeness of Trametes villosa CCMB561 and Reveals a Huge Potential for Lignocellulose Breakdown. J Fungi (Basel) 2022; 8:jof8020142. [PMID: 35205897 PMCID: PMC8876698 DOI: 10.3390/jof8020142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Trametes villosa is a wood-decaying fungus with great potential to be used in the bioconversion of agro-industrial residues and to obtain high-value-added products, such as biofuels. Nonetheless, the lack of high-quality genomic data hampers studies investigating genetic mechanisms and metabolic pathways in T. villosa, hindering its application in industry. Herein, applying a hybrid assembly pipeline using short reads (Illumina HiSeq) and long reads (Oxford Nanopore MinION), we obtained a high-quality genome for the T. villosa CCMB561 and investigated its genetic potential for lignocellulose breakdown. The new genome possesses 143 contigs, N50 of 1,009,271 bp, a total length of 46,748,415 bp, 14,540 protein-coding genes, 22 secondary metabolite gene clusters, and 426 genes encoding Carbohydrate-Active enzymes. Our CAZome annotation and comparative genomic analyses of nine Trametes spp. genomes revealed T. villosa CCMB561 as the species with the highest number of genes encoding lignin-modifying enzymes and a wide array of genes encoding proteins for the breakdown of cellulose, hemicellulose, and pectin. These results bring to light the potential of this isolate to be applied in the bioconversion of lignocellulose and will support future studies on the expression, regulation, and evolution of genes, proteins, and metabolic pathways regarding the bioconversion of lignocellulosic residues.
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Affiliation(s)
- Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Felipe Ferreira da Silva
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Paula Luize Camargos Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Thairine Mendes-Pereira
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Vasco Ariston de Carvalho Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, 37073 Göttingen, Germany;
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte 30421-169, MG, Brazil;
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
- Correspondence: ; Tel.: +55-31-994130996
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170
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Lan T, Fang D, Li H, Sahu SK, Wang Q, Yuan H, Zhu Y, Yang Z, Zhang L, Yang S, Lu H, Han L, Zhang S, Yu J, Mahmmod YS, Xu Y, Hua Y, He F, Yuan Z, Liu H. Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution. Front Genet 2022; 12:819493. [PMID: 35126472 PMCID: PMC8815822 DOI: 10.3389/fgene.2021.819493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 12/08/2021] [Indexed: 12/22/2022] Open
Abstract
The masked palm civet (Paguma larvata) is a small carnivore with distinct biological characteristics, that likes an omnivorous diet and also serves as a vector of pathogens. Although this species is not an endangered animal, its population is reportedly declining. Since the severe acute respiratory syndrome (SARS) epidemic in 2003, the public has been particularly concerned about this species. Here, we present the first genome of the P. larvata, comprising 22 chromosomes assembled using single-tube long fragment read (stLFR) and Hi-C technologies. The genome length is 2.41 Gb with a scaffold N50 of 105.6 Mb. We identified the 107.13 Mb X chromosome and one 1.34 Mb Y-linked scaffold and validated them by resequencing 45 P. larvata individuals. We predicted 18,340 protein-coding genes, among which 18,333 genes were functionally annotated. Interestingly, several biological pathways related to immune defenses were found to be significantly expanded. Also, more than 40% of the enriched pathways on the positively selected genes (PSGs) were identified to be closely related to immunity and survival. These enriched gene families were inferred to be essential for the P. larvata for defense against the pathogens. However, we did not find a direct genomic basis for its adaptation to omnivorous diet despite multiple attempts of comparative genomic analysis. In addition, we evaluated the susceptibility of the P. larvata to the SARS-CoV-2 by screening the RNA expression of the ACE2 and TMPRSS2/TMPRSS4 genes in 16 organs. Finally, we explored the genome-wide heterozygosity and compared it with other animals to evaluate the population status of this species. Taken together, this chromosome-scale genome of the P. larvata provides a necessary resource and insights for understanding the genetic basis of its biological characteristics, evolution, and disease transmission control.
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Affiliation(s)
- Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yixin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zipeng Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Le Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shangchen Yang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shaofang Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Jieyao Yu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Yasser S. Mahmmod
- Department of Veterinary Sciences, Faculty of Health Sciences, Higher Colleges of Technology, Al Ain, United Arab Emirates
- Division of Infectious Diseases, Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Yan Hua
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Fengping He
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- *Correspondence: Huan Liu, ; Ziguo Yuan, ; Fengping He,
| | - Ziguo Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- *Correspondence: Huan Liu, ; Ziguo Yuan, ; Fengping He,
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
- *Correspondence: Huan Liu, ; Ziguo Yuan, ; Fengping He,
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171
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Smolander OP, Blande D, Ahola V, Rastas P, Tanskanen J, Kammonen JI, Oostra V, Pellegrini L, Ikonen S, Dallas T, DiLeo MF, Duplouy A, Duru IC, Halimaa P, Kahilainen A, Kuwar SS, Kärenlampi SO, Lafuente E, Luo S, Makkonen J, Nair A, de la Paz Celorio-Mancera M, Pennanen V, Ruokolainen A, Sundell T, Tervahauta AI, Twort V, van Bergen E, Österman-Udd J, Paulin L, Frilander MJ, Auvinen P, Saastamoinen M. Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map. Gigascience 2022; 11:6505122. [PMID: 35022701 PMCID: PMC8756199 DOI: 10.1093/gigascience/giab097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/03/2021] [Accepted: 12/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. RESULTS The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92-94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. CONCLUSIONS The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.
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Affiliation(s)
- Olli-Pekka Smolander
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland.,Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Daniel Blande
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Virpi Ahola
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland.,Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, 171 77 Stockholm, Hong Kong
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | | | - Juhana I Kammonen
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Vicencio Oostra
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland.,Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool CH64 7TE, UK
| | - Lorenzo Pellegrini
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Suvi Ikonen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Tad Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michelle F DiLeo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Anne Duplouy
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Ilhan Cem Duru
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Pauliina Halimaa
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 KUOPIO, Finland
| | - Aapo Kahilainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Suyog S Kuwar
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611-0620, USA.,Department of Zoology, Loknete Vyankatrao Hiray Arts, Science & Commerce College, 422003, Maharashtra, India
| | - Sirpa O Kärenlampi
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 KUOPIO, Finland
| | - Elvira Lafuente
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Shiqi Luo
- College of Plant Protection, China Agricultural University, Beijing 100083, China
| | - Jenny Makkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 KUOPIO, Finland
| | - Abhilash Nair
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | | | - Ville Pennanen
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Annukka Ruokolainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Tarja Sundell
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Arja I Tervahauta
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 KUOPIO, Finland
| | - Victoria Twort
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Erik van Bergen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Janina Österman-Udd
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Marjo Saastamoinen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland.,Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
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172
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Ríos-Touma B, Holzenthal RW, Rázuri-Gonzales E, Heckenhauer J, Pauls SU, Storer CG, Frandsen PB. De Novo Genome Assembly and Annotation of an Andean Caddisfly, Atopsyche davidsoni Sykora, 1991, a Model for Genome Research of High-Elevation Adaptations. Genome Biol Evol 2022; 14:evab286. [PMID: 34962985 PMCID: PMC8767365 DOI: 10.1093/gbe/evab286] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
We sequence, assemble, and annotate the genome of Atopsyche davidsoni Sykora, 1991, the first whole-genome assembly for the caddisfly family Hydrobiosidae. This free-living and predatory caddisfly inhabits streams in the high-elevation Andes and is separated by more than 200 Myr of evolutionary history from the most closely related caddisfly species with genome assemblies available. We demonstrate the promise of PacBio HiFi reads by assembling the most contiguous caddisfly genome assembly to date with a contig N50 of 14 Mb, which is more than 6× more contiguous than the current most contiguous assembly for a caddisfly (Hydropsyche tenuis). We recover 98.8% of insect BUSCO genes indicating a high level of gene completeness. We also provide a genome annotation of 12,232 annotated proteins. This new genome assembly provides an important new resource for studying genomic adaptation of aquatic insects to harsh, high-altitude environments.
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Affiliation(s)
- Blanca Ríos-Touma
- Facultad de Ingenierías y Ciencias Aplicadas, Ingeniería Ambiental, Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
| | - Ralph W Holzenthal
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, USA
| | - Ernesto Rázuri-Gonzales
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, USA
- Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Germany
| | - Jacqueline Heckenhauer
- Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Steffen U Pauls
- Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Institute of Insect Biotechnology, Justus-Liebig University, Gießen, Germany
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Paul B Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
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173
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Piombo E, Dubey M. Computational Analysis of HTS Data and Its Application in Plant Pathology. Methods Mol Biol 2022; 2536:275-307. [PMID: 35819611 DOI: 10.1007/978-1-0716-2517-0_17] [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: 06/15/2023]
Abstract
High-throughput sequencing is a basic tool of biological research, and it is extensively used in plant pathology projects. Here, we describe how to handle data coming from a variety of sequencing experiments, focusing on the analysis of Illumina reads. We describe how to perform genome assembly and annotation with DNA reads, correctly analyze RNA-seq data to discover differentially expressed genes, handle amplicon sequencing data from microbial communities, and utilize small RNA sequencing data to predict miRNA sequences and their putative targets.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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174
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Zhang X, Lin C, Li H, Liu S, Wang Q, Yang S, Shi M, Sahu SK, Zhu Y, Wang J, Huang J, Hu Y, Yu J, Zhang S, Li G, Guan W, Lu H, Lan T, Xu Y. OUP accepted manuscript. Genome Biol Evol 2022; 14:6519822. [PMID: 35106558 PMCID: PMC8857919 DOI: 10.1093/gbe/evac015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
The green peafowl (Pavo muticus) is facing a high risk of extinction due to the long-term and widespread threats of poaching and habitat conversion. Here, we present a high-quality chromosome-level genome assembly of the green peafowl with high contiguity and accuracy assembled by PacBio sequencing, DNBSEQ short-read sequencing, and Hi-C sequencing technologies. The final genome size was estimated to be 1.049 Gb, whereas 1.042 Gb of the genome was assigned to 27 pseudochromosomes. The scaffold N50 length was 75.5 Mb with a complete BUSCO score of 97.6%. We identified W and Z chromosomes and validated them by resequencing 14 additional individuals. Totally, 167.04 Mb repetitive elements were identified in the genome, accounting for 15.92% of the total genome size. We predicted 14,935 protein-coding genes, among which 14,931 genes were functionally annotated. This is the most comprehensive and complete de novo assembly of the Pavo genus, and it will serve as a valuable resource for future green peafowl ecology, evolution, and conservation studies.
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Affiliation(s)
- Xinyuan Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Chuyu Lin
- Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen, R & D Center, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Sixia Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shangchen Yang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yixin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiangang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Junxuan Huang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yiyin Hu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Jieyao Yu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Shaofang Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Guanglong Li
- China National Forestry Industry Federation, Beijing, China
| | - Wenyuan Guan
- Quzhou Yueniao Agricultural Development Co. Ltd, Quzhou, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
- Corresponding authors: E-mails: ; ;
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Corresponding authors: E-mails: ; ;
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- Corresponding authors: E-mails: ; ;
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175
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Xu H, Wang C, Shao G, Wu S, Liu P, Cao P, Jiang P, Wang S, Zhu H, Lin X, Tauqeer A, Lin Y, Chen W, Huang W, Wen Q, Chang J, Zhong F, Wu S. The reference genome and full-length transcriptome of pakchoi provide insights into cuticle formation and heat adaption. HORTICULTURE RESEARCH 2022; 9:uhac123. [PMID: 35949690 PMCID: PMC9358696 DOI: 10.1093/hr/uhac123] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/17/2022] [Indexed: 05/20/2023]
Abstract
Brassica rapa includes various vegetables with high economic value. Among them, green petiole type pakchoi (B. rapa ssp. chinensis) is one of the major vegetables grown in southern China. Compared with other B. rapa varieties, green petiole type pakchoi shows a higher level of heat resistance, which is partially derived from the rich epicuticular wax. Here we sequence a high-quality genome of green petiole type pakchoi, which has been widely used as the parent in breeding. Our results reveal that long terminal repeat retrotransposon insertion plays critical roles in promoting the genome expansion and transcriptional diversity of pakchoi genes through preferential insertions, particularly in cuticle biosynthetic genes. After whole-genome triplication, over-retained pakchoi genes escape stringent selection pressure, and among them a set of cuticle-related genes are retained. Using bulked-segregant analysis of a heat-resistant pakchoi cultivar, we identify a frame-shift deletion across the third exon and the subsequent intron of BrcCER1 in candidate regions. Using Nanopore long-read sequencing, we analyze the full-length transcriptome of two pakchoi cultivars with opposite sensitivity to high temperature. We find that the heat-resistant pakchoi cultivar can mitigate heat-caused leaf damage by activating an unfolded protein response, as well as by inhibiting chloroplast development and energy metabolism, which are presumably mediated by both transcriptional regulation and splicing factors. Our study provides valuable resources for Brassica functional genomics and breeding research, and deepens our understanding of plant stress resistance.
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Affiliation(s)
| | | | | | - Shasha Wu
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Liu
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ping Cao
- Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou 350000, China
| | - Peng Jiang
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shubin Wang
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Zhu
- Fujian Seed Chief Station, Fuzhou 350003, China
| | - Xiao Lin
- Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou 350000, China
| | - Arfa Tauqeer
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yizhang Lin
- Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou 350000, China
| | - Wei Chen
- Fujian Seed Chief Station, Fuzhou 350003, China
| | | | - Qingfang Wen
- Crop Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Jiang Chang
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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176
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Francisco FR, Aono AH, da Silva CC, Gonçalves PS, Scaloppi Junior EJ, Le Guen V, Fritsche-Neto R, Souza LM, de Souza AP. Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches. FRONTIERS IN PLANT SCIENCE 2021; 12:768589. [PMID: 34992619 PMCID: PMC8724537 DOI: 10.3389/fpls.2021.768589] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/02/2021] [Indexed: 06/08/2023]
Abstract
Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs.
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Affiliation(s)
- Felipe Roberto Francisco
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla Cristina da Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Paulo S. Gonçalves
- Center of Rubber Tree and Agroforestry Systems, Agronomic Institute (IAC), Votuporanga, Brazil
| | | | - Vincent Le Guen
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Roberto Fritsche-Neto
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Livia Moura Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- São Francisco University (USF), Itatiba, Brazil
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
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177
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Sigeman H, Strandh M, Proux-Wéra E, Kutschera VE, Ponnikas S, Zhang H, Lundberg M, Soler L, Bunikis I, Tarka M, Hasselquist D, Nystedt B, Westerdahl H, Hansson B. Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration. Mol Biol Evol 2021; 38:5275-5291. [PMID: 34542640 PMCID: PMC8662655 DOI: 10.1093/molbev/msab277] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (My) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event ∼24 Ma formed "neo-sex chromosomes" consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and whereas the added-Z has retained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for nonrandom maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex linkage.
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Affiliation(s)
- Hanna Sigeman
- Department of Biology, Lund University, Lund, Sweden
| | - Maria Strandh
- Department of Biology, Lund University, Lund, Sweden
| | - Estelle Proux-Wéra
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Suvi Ponnikas
- Department of Biology, Lund University, Lund, Sweden
| | - Hongkai Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Genome Center, Uppsala University, Uppsala, Sweden
| | - Maja Tarka
- Department of Biology, Lund University, Lund, Sweden
| | | | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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178
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Oh DH, Kowalski KP, Quach QN, Wijesinghege C, Tanford P, Dassanayake M, Clay K. Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed). Mol Ecol 2021; 31:1142-1159. [PMID: 34839548 PMCID: PMC9300010 DOI: 10.1111/mec.16293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/12/2021] [Accepted: 11/15/2021] [Indexed: 11/06/2022]
Abstract
The rapid invasion of the non‐native Phragmites australis (Poaceae, subfamily Arundinoideae) is a major threat to native wetland ecosystems in North America and elsewhere. We describe the first reference genome for P. australis and compare invasive (ssp. australis) and native (ssp. americanus) genotypes collected from replicated populations across the Laurentian Great Lakes to deduce genomic bases driving its invasive success. Here, we report novel genomic features including a Phragmites lineage‐specific whole genome duplication, followed by gene loss and preferential retention of genes associated with transcription factors and regulatory functions in the remaining duplicates. Comparative transcriptomic analyses revealed that genes associated with biotic stress and defence responses were expressed at a higher basal level in invasive genotypes, but native genotypes showed a stronger induction of defence responses when challenged by a fungal endophyte. The reference genome and transcriptomes, combined with previous ecological and environmental data, add to our understanding of mechanisms leading to invasiveness and support the development of novel, genomics‐assisted management approaches for invasive Phragmites.
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Affiliation(s)
- Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Kurt P Kowalski
- U.S. Geological Survey, Great Lakes Science Center, Ann Arbor, Michigan, USA
| | - Quynh N Quach
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
| | - Chathura Wijesinghege
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Philippa Tanford
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Keith Clay
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA.,Department of Biology, Indiana University, Bloomington, Indiana, USA
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179
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Guo X, Fang D, Sahu SK, Yang S, Guang X, Folk R, Smith SA, Chanderbali AS, Chen S, Liu M, Yang T, Zhang S, Liu X, Xu X, Soltis PS, Soltis DE, Liu H. Chloranthus genome provides insights into the early diversification of angiosperms. Nat Commun 2021; 12:6930. [PMID: 34836973 PMCID: PMC8626473 DOI: 10.1038/s41467-021-26922-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.
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Affiliation(s)
- Xing Guo
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Dongming Fang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Sunil Kumar Sahu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shuai Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Xuanmin Guang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ryan Folk
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762 United States of America
| | - Stephen A. Smith
- grid.214458.e0000000086837370Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 United States of America
| | - Andre S. Chanderbali
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Sisi Chen
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.9227.e0000000119573309South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650 China
| | - Min Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ting Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shouzhou Zhang
- grid.9227.e0000000119573309Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, Chinese Academy of Sciences, Shenzhen, 518004 China
| | - Xin Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839BGI-Fuyang, BGI-Shenzhen, Fuyang, 236009 China
| | - Xun Xu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518083 China
| | - Pamela S. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Douglas E. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America ,grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, FL 32611 United States of America
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
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180
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Draft Genome Sequence of Mortierella alpina Strain LL118, Isolated from an Aspen (Populus tremuloides) Leaf Litter Sample. Microbiol Resour Announc 2021; 10:e0086421. [PMID: 34817213 PMCID: PMC8612081 DOI: 10.1128/mra.00864-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mortierella alpina is a filamentous fungus commonly associated with soil and is one of very few fungal species known to include strains with ice nucleation activity. Here, we report the draft genome sequence of the ice nucleation-active M. alpina strain LL118, isolated from aspen leaf litter collected in Alberta, Canada.
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181
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Scalzitti N, Kress A, Orhand R, Weber T, Moulinier L, Jeannin-Girardon A, Collet P, Poch O, Thompson JD. Spliceator: multi-species splice site prediction using convolutional neural networks. BMC Bioinformatics 2021; 22:561. [PMID: 34814826 PMCID: PMC8609763 DOI: 10.1186/s12859-021-04471-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
Background Ab initio prediction of splice sites is an essential step in eukaryotic genome annotation. Recent predictors have exploited Deep Learning algorithms and reliable gene structures from model organisms. However, Deep Learning methods for non-model organisms are lacking. Results We developed Spliceator to predict splice sites in a wide range of species, including model and non-model organisms. Spliceator uses a convolutional neural network and is trained on carefully validated data from over 100 organisms. We show that Spliceator achieves consistently high accuracy (89–92%) compared to existing methods on independent benchmarks from human, fish, fly, worm, plant and protist organisms. Conclusions Spliceator is a new Deep Learning method trained on high-quality data, which can be used to predict splice sites in diverse organisms, ranging from human to protists, with consistently high accuracy. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04471-3.
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Affiliation(s)
- Nicolas Scalzitti
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Arnaud Kress
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France.,BiGEst-ICube Platform, ICube Laboratory, UMR7357, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Romain Orhand
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Thomas Weber
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Luc Moulinier
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France.,BiGEst-ICube Platform, ICube Laboratory, UMR7357, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Anne Jeannin-Girardon
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Pierre Collet
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Olivier Poch
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Julie D Thompson
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France.
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182
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Zhang Q, Tombline G, Ablaeva J, Zhang L, Zhou X, Smith Z, Zhao Y, Xiaoli AM, Wang Z, Lin JR, Jabalameli MR, Mitra J, Nguyen N, Vijg J, Seluanov A, Gladyshev VN, Gorbunova V, Zhang ZD. Genomic expansion of Aldh1a1 protects beavers against high metabolic aldehydes from lipid oxidation. Cell Rep 2021; 37:109965. [PMID: 34758328 PMCID: PMC8656434 DOI: 10.1016/j.celrep.2021.109965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 06/07/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022] Open
Abstract
The North American beaver is an exceptionally long-lived and cancer-resistant rodent species. Here, we report the evolutionary changes in its gene coding sequences, copy numbers, and expression. We identify changes that likely increase its ability to detoxify aldehydes, enhance tumor suppression and DNA repair, and alter lipid metabolism, potentially contributing to its longevity and cancer resistance. Hpgd, a tumor suppressor gene, is uniquely duplicated in beavers among rodents, and several genes associated with tumor suppression and longevity are under positive selection in beavers. Lipid metabolism genes show positive selection signals, changes in copy numbers, or altered gene expression in beavers. Aldh1a1, encoding an enzyme for aldehydes detoxification, is particularly notable due to its massive expansion in beavers, which enhances their cellular resistance to ethanol and capacity to metabolize diverse aldehyde substrates from lipid oxidation and their woody diet. We hypothesize that the amplification of Aldh1a1 may contribute to the longevity of beavers. Zhang et al. examine the genome of North American beavers and find evolutionary changes that could contribute to beavers’ longevity. In particular, Aldh1a1, encoding an enzyme for aldehyde detoxification, is massively expanded in the beaver genome, protecting them against exposure to aldehydes from lipid oxidation and their woody diet.
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Affiliation(s)
- Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gregory Tombline
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zachary Smith
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alus M Xiaoli
- Departments of Medicine and Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhen Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - M Reza Jabalameli
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nha Nguyen
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
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183
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Cornet L, D'hooge E, Magain N, Stubbe D, Packeu A, Baurain D, Becker P. The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach. Microb Genom 2021; 7. [PMID: 34730487 PMCID: PMC8743564 DOI: 10.1099/mgen.0.000707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex.
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Affiliation(s)
- Luc Cornet
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - Elizabet D'hooge
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - Nicolas Magain
- InBioS, Evolution and Conservation Biology, University of Liège, Liège, Belgium
| | - Dirk Stubbe
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - Ann Packeu
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - Denis Baurain
- InBioS, PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Pierre Becker
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
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184
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Perkin LC, Bell A, Hinze LL, Suh CPC, Arick MA, Peterson DG, Udall JA. Genome assembly of two nematode-resistant cotton lines ( Gossypium hirsutum L.). G3 GENES|GENOMES|GENETICS 2021; 11. [PMID: 34849785 PMCID: PMC8527472 DOI: 10.1093/g3journal/jkab276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Abstract
Upland cotton (Gossypium hirsutum L.) is susceptible to damage by the root-knot and the reniform nematodes, causing yield losses greater than 4% annually in the United States. In addition, these nematodes are synergistic with seeding disease and root rot pathogens that exacerbate diseases and subsequent yield losses. Production practices to minimize nematode damage include crop rotation and nematicides, but these techniques need to be repeated and are expensive. The use of resistant cultivars is deemed the most effective and economical approach for managing nematodes in cotton. Here, we describe the genomes of two nematode-resistant lines of cotton, BARBREN-713 and BAR 32-30. These genomes may expedite the development of DNA markers that can be used to efficiently introduce nematode resistance into commercially valuable Upland lines.
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Affiliation(s)
- Lindsey C Perkin
- USDA Agricultural Research Service, Insect Control and Cotton Disease Research Unit, College Station, TX 77845, USA
| | - Al Bell
- USDA Agricultural Research Service, Insect Control and Cotton Disease Research Unit, College Station, TX 77845, USA
| | - Lori L Hinze
- USDA Agricultural Research Service, Crop Germplasm Research Unit, College Station, TX 77845, USA
| | - Charles P -C Suh
- USDA Agricultural Research Service, Insect Control and Cotton Disease Research Unit, College Station, TX 77845, USA
| | - Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Joshua A Udall
- USDA Agricultural Research Service, Crop Germplasm Research Unit, College Station, TX 77845, USA
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185
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Yang X, Gao S, Guo L, Wang B, Jia Y, Zhou J, Che Y, Jia P, Lin J, Xu T, Sun J, Ye K. Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nat Commun 2021; 12:6030. [PMID: 34654815 PMCID: PMC8521590 DOI: 10.1038/s41467-021-26330-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 09/29/2021] [Indexed: 01/07/2023] Open
Abstract
For millions of years, plants evolve plenty of structurally diverse secondary metabolites (SM) to support their sessile lifestyles through continuous biochemical pathway innovation. While new genes commonly drive the evolution of plant SM pathway, how a full biosynthetic pathway evolves remains poorly understood. The evolution of pathway involves recruiting new genes along the reaction cascade forwardly, backwardly, or in a patchwork manner. With three chromosome-scale Papaver genome assemblies, we here reveal whole-genome duplications (WGDs) apparently accelerate chromosomal rearrangements with a nonrandom distribution towards SM optimization. A burst of structural variants involving fusions, translocations and duplications within 7.7 million years have assembled nine genes into the benzylisoquinoline alkaloids gene cluster, following a punctuated patchwork model. Biosynthetic gene copies and their total expression matter to morphinan production. Our results demonstrate how new genes have been recruited from a WGD-induced repertoire of unregulated enzymes with promiscuous reactivities to innovate efficient metabolic pathways with spatiotemporal constraint.
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Affiliation(s)
- Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shenghan Gao
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Li Guo
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yanyan Jia
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jian Zhou
- College of Life Sciences, Henan Normal University, Xinxiang, Henan, China
| | - Yizhuo Che
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Peng Jia
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jiadong Lin
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Tun Xu
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jianyong Sun
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Kai Ye
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,Faculty of Science, Leiden University, Leiden, The Netherlands.
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186
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Chakraborty A, Mahajan S, Jaiswal SK, Sharma VK. Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. Commun Biol 2021; 4:1193. [PMID: 34654884 PMCID: PMC8521574 DOI: 10.1038/s42003-021-02720-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 08/13/2021] [Indexed: 12/28/2022] Open
Abstract
Curcuma longa, or turmeric, is traditionally known for its immense medicinal properties and has diverse therapeutic applications. However, the absence of a reference genome sequence is a limiting factor in understanding the genomic basis of the origin of its medicinal properties. In this study, we present the draft genome sequence of C. longa, belonging to Zingiberaceae plant family, constructed using 10x Genomics linked reads and Oxford Nanopore long reads. For comprehensive gene set prediction and for insights into its gene expression, transcriptome sequencing of leaf tissue was also performed. The draft genome assembly had a size of 1.02 Gbp with ~70% repetitive sequences, and contained 50,401 coding gene sequences. The phylogenetic position of C. longa was resolved through a comprehensive genome-wide analysis including 16 other plant species. Using 5,388 orthogroups, the comparative evolutionary analysis performed across 17 species including C. longa revealed evolution in genes associated with secondary metabolism, plant phytohormones signaling, and various biotic and abiotic stress tolerance responses. These mechanisms are crucial for perennial and rhizomatous plants such as C. longa for defense and environmental stress tolerance via production of secondary metabolites, which are associated with the wide range of medicinal properties in C. longa.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shubham K Jaiswal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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187
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Alabi N, Wu Y, Bossdorf O, Rieseberg LH, Colautti RI. Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics. G3-GENES GENOMES GENETICS 2021; 11:6380431. [PMID: 34599816 PMCID: PMC8664459 DOI: 10.1093/g3journal/jkab339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/10/2021] [Indexed: 11/24/2022]
Abstract
The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here, we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara and Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy, and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one-third of BUSCO genes (390/1440) mapped to two or more scaffolds despite <2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.
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Affiliation(s)
- Nikolay Alabi
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Yihan Wu
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Oliver Bossdorf
- Institute of Ecology and Evolution, University of Tübingen, 72074 Tübingen, Germany
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Robert I Colautti
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
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188
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Brandt A, Tran Van P, Bluhm C, Anselmetti Y, Dumas Z, Figuet E, François CM, Galtier N, Heimburger B, Jaron KS, Labédan M, Maraun M, Parker DJ, Robinson-Rechavi M, Schaefer I, Simion P, Scheu S, Schwander T, Bast J. Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova. Proc Natl Acad Sci U S A 2021; 118:e2101485118. [PMID: 34535550 PMCID: PMC8463897 DOI: 10.1073/pnas.2101485118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/05/2022] Open
Abstract
Sex strongly impacts genome evolution via recombination and segregation. In the absence of these processes, haplotypes within lineages of diploid organisms are predicted to accumulate mutations independently of each other and diverge over time. This so-called "Meselson effect" is regarded as a strong indicator of the long-term evolution under obligate asexuality. Here, we present genomic and transcriptomic data of three populations of the asexual oribatid mite species Oppiella nova and its sexual relative Oppiella subpectinata We document strikingly different patterns of haplotype divergence between the two species, strongly supporting Meselson effect-like evolution and long-term asexuality in O. nova: I) variation within individuals exceeds variation between populations in O. nova but vice versa in O. subpectinata; II) two O. nova sublineages feature a high proportion of lineage-specific heterozygous single-nucleotide polymorphisms (SNPs), indicating that haplotypes continued to diverge after lineage separation; III) the deepest split in gene trees generally separates the two haplotypes in O. nova, but populations in O. subpectinata; and IV) the topologies of the two haplotype trees match each other. Our findings provide positive evidence for the absence of canonical sex over evolutionary time in O. nova and suggest that asexual oribatid mites can escape the dead-end fate usually associated with asexual lineages.
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Affiliation(s)
- Alexander Brandt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany;
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christian Bluhm
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
- Abteilung Boden und Umwelt, Forstliche Versuchs- und Forschungsanstalt Baden-Wuerttemberg, 79100 Freiburg, Germany
| | - Yoann Anselmetti
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
- CoBIUS Lab, Department of Computer Science, University of Sherbrooke, Sherbrooke, QC J1K2R1, Canada
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Emeric Figuet
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
| | - Clémentine M François
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, École Nationale des Travaux Publics de l'État, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France
| | - Nicolas Galtier
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
| | - Bastian Heimburger
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Marjorie Labédan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mark Maraun
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ina Schaefer
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
| | - Paul Simion
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
- Laboratory of Evolutionary Genetics and Ecology, Unit in Environmental and Evolutionary Biology, Université de Namur, 5000 Namur, Belgium
| | - Stefan Scheu
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
- Section Biodiversity and Ecology, Centre of Biodiversity and Sustainable Land Use, 37073 Goettingen, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Institute for Zoology, University of Cologne, 50674 Cologne, Germany
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189
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Freire R, Weisweiler M, Guerreiro R, Baig N, Hüttel B, Obeng-Hinneh E, Renner J, Hartje S, Muders K, Truberg B, Rosen A, Prigge V, Bruckmüller J, Lübeck J, Stich B. Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety. G3-GENES GENOMES GENETICS 2021; 11:6371871. [PMID: 34534288 PMCID: PMC8664475 DOI: 10.1093/g3journal/jkab330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/08/2021] [Indexed: 01/27/2023]
Abstract
Potato (Solanum tuberosum L.) is one of the most important crops with a worldwide production of 370 million metric tons. The objectives of this study were (1) to create a high-quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (2) to evaluate the new assembly’s usefulness for various genomic methods; and (3) to assess the performance of phasing in diploid and tetraploid clones, using linked-read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.
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Affiliation(s)
- Ruth Freire
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Marius Weisweiler
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ricardo Guerreiro
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Nadia Baig
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Bruno Hüttel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding, Carl-von-Linne-Weg 10, 50829 Köln, Germany
| | - Evelyn Obeng-Hinneh
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Strehlow 19, 17111 Hohenmocker, Germany
| | - Juliane Renner
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Strehlow 19, 17111 Hohenmocker, Germany
| | - Stefanie Hartje
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Strehlow 19, 17111 Hohenmocker, Germany
| | - Katja Muders
- Nordring- Kartoffelzucht- und Vermehrungs- GmbH, Parkweg 4, 18190 Sanitz, Germany
| | - Bernd Truberg
- Nordring- Kartoffelzucht- und Vermehrungs- GmbH, Parkweg 4, 18190 Sanitz, Germany
| | - Arne Rosen
- Nordring- Kartoffelzucht- und Vermehrungs- GmbH, Parkweg 4, 18190 Sanitz, Germany
| | - Vanessa Prigge
- SaKa Pflanzenzucht GmbH & Co. KG, Zuchtstation Windeby, Eichenallee 9, 24340 Windeby, Germany
| | | | - Jens Lübeck
- Solana Research GmbH, Eichenallee 9, 24340 Windeby, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany.,Cluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, Universitätsstraße 1, 40225 Düsseldorf, Germany
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190
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Phylogeographic reconstruction of the marbled crayfish origin. Commun Biol 2021; 4:1096. [PMID: 34535758 PMCID: PMC8448756 DOI: 10.1038/s42003-021-02609-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/20/2021] [Indexed: 11/08/2022] Open
Abstract
The marbled crayfish (Procambarus virginalis) is a triploid and parthenogenetic freshwater crayfish species that has colonized diverse habitats around the world. Previous studies suggested that the clonal marbled crayfish population descended as recently as 25 years ago from a single specimen of P. fallax, the sexually reproducing parent species. However, the genetic, phylogeographic, and mechanistic origins of the species have remained enigmatic. We have now constructed a new genome assembly for P. virginalis to support a detailed phylogeographic analysis of the diploid parent species, Procambarus fallax. Our results strongly suggest that both parental haplotypes of P. virginalis were inherited from the Everglades subpopulation of P. fallax. Comprehensive whole-genome sequencing also detected triploid specimens in the same subpopulation, which either represent evolutionarily important intermediate genotypes or independent parthenogenetic lineages arising among the sexual parent population. Our findings thus clarify the geographic origin of the marbled crayfish and identify potential mechanisms of parthenogenetic speciation.
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191
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Bachvaroff TR, McDonald RC, Plough LV, Chung JS. Chromosome-level genome assembly of the blue crab, Callinectes sapidus. G3-GENES GENOMES GENETICS 2021; 11:6304867. [PMID: 34544121 PMCID: PMC8496215 DOI: 10.1093/g3journal/jkab212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 11/14/2022]
Abstract
The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200× coverage Illumina paired-end reads, a 60× 8 kb mate-paired library, and 50× PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The 50 largest scaffolds span 810 Mb are 1.5-37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10 kb with a repeat content of 68%. The final assembly N50 is 18.9 Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, ∼88% (888/1013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but 9 scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, of which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species.
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Affiliation(s)
- Tsvetan R Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Ryan C McDonald
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Louis V Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Horn Point, MD 21613, USA
| | - J Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
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192
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Wu Z, Liu H, Zhan W, Yu Z, Qin E, Liu S, Yang T, Xiang N, Kudrna D, Chen Y, Lee S, Li G, Wing RA, Liu J, Xiong H, Xia C, Xing Y, Zhang J, Qin R. The chromosome-scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1725-1742. [PMID: 33768699 PMCID: PMC8428823 DOI: 10.1111/pbi.13586] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/08/2021] [Accepted: 03/16/2021] [Indexed: 05/04/2023]
Abstract
Safflower (Carthamus tinctorius L.), a member of the Asteraceae, is a popular crop due to its high linoleic acid (LA) and flavonoid (such as hydroxysafflor yellow A) contents. Here, we report the first high-quality genome assembly (contig N50 of 21.23 Mb) for the 12 pseudochromosomes of safflower using single-molecule real-time sequencing, Hi-C mapping technologies and a genetic linkage map. Phyloge nomic analysis showed that safflower diverged from artichoke (Cynara cardunculus) and sunflower (Helianthus annuus) approximately 30.7 and 60.5 million years ago, respectively. Comparative genomic analyses revealed that uniquely expanded gene families in safflower were enriched for those predicted to be involved in lipid metabolism and transport and abscisic acid signalling. Notably, the fatty acid desaturase 2 (FAD2) and chalcone synthase (CHS) families, which function in the LA and flavonoid biosynthesis pathways, respectively, were expanded via tandem duplications in safflower. CarFAD2-12 was specifically expressed in seeds and was vital for high-LA content in seeds, while tandemly duplicated CarFAD2 genes were up-regulated in ovaries compared to CarFAD2-12, which indicates regulatory divergence of FAD2 in seeds and ovaries. CarCHS1, CarCHS4 and tandem-duplicated CarCHS5˜CarCHS6, which were up-regulated compared to other CarCHS members at early stages, contribute to the accumulation of major flavonoids in flowers. In addition, our data reveal multiple alternative splicing events in gene families related to fatty acid and flavonoid biosynthesis. Together, these results provide a high-quality reference genome and evolutionary insights into the molecular basis of fatty acid and flavonoid biosynthesis in safflower.
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Affiliation(s)
- Zhihua Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Wei Zhan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Zhichao Yu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Erdai Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Niyan Xiang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Dave Kudrna
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
| | - Yan Chen
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Seunghee Lee
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
| | - Gang Li
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Rod A. Wing
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Jiao Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Hairong Xiong
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
| | - Chunjiao Xia
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of ChinaKey Laboratory of State Ethnic Affairs Commission for Biological TechnologyCollege of Life SciencesSouth‐Central University for NationalitiesWuhanChina
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193
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Thompson AW, Hawkins MB, Parey E, Wcisel DJ, Ota T, Kawasaki K, Funk E, Losilla M, Fitch OE, Pan Q, Feron R, Louis A, Montfort J, Milhes M, Racicot BL, Childs KL, Fontenot Q, Ferrara A, David SR, McCune AR, Dornburg A, Yoder JA, Guiguen Y, Roest Crollius H, Berthelot C, Harris MP, Braasch I. The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nat Genet 2021; 53:1373-1384. [PMID: 34462605 PMCID: PMC8423624 DOI: 10.1038/s41588-021-00914-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.
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Affiliation(s)
- Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - M Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Research, Boston Children's Hospital, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Elise Parey
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, SOKENDAI (the Graduate University for Advanced Studies), Hayama, Japan
| | - Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Emily Funk
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Animal Science Department, University of California Davis, Davis, CA, USA
| | - Mauricio Losilla
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Olivia E Fitch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Qiaowei Pan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra Louis
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | | | - Marine Milhes
- GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France
| | - Brett L Racicot
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Solomon R David
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
- Comparative Medicine Institute, NC State University, Raleigh, NC, USA
- Center for Human Health and the Environment, NC State University, Raleigh, NC, USA
| | | | - Hugues Roest Crollius
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Research, Boston Children's Hospital, Boston, MA, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA.
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194
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Hao Z, Li Y, Jiang Y, Xu J, Li J, Luo L. Genome Sequence Analysis of the Fungal Pathogen Fusarium graminearum Using Oxford Nanopore Technology. J Fungi (Basel) 2021; 7:jof7090699. [PMID: 34575738 PMCID: PMC8465144 DOI: 10.3390/jof7090699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Fusarium graminearum is a plant pathogen of global importance which causes not only significant yield loss but also crop spoilage due to mycotoxins that render grain unsafe for human or livestock consumption. Although the full genome of several F. graminearum isolates from different parts of the world have been sequenced, there are no similar studies of isolates originating from China. The current study sought to address this by sequencing the F. graminearum isolate FG-12, which was isolated from the roots of maize seedlings exhibiting typical symptoms of blight growing in the Gansu province, China, using Oxford Nanopore Technology (ONT). The FG-12 isolate was found to have a 35.9 Mb genome comprised of five scaffolds corresponding to the four chromosomes and mitochondrial DNA of the F. graminearum type strain, PH-1. The genome was found to contain an approximately 2.23% repetitive sequence and encode 12,470 predicted genes. Additional bioinformatic analysis identified 437 genes that were predicted to be secreted effectors, one of which was confirmed to trigger a hypersensitive responses (HR) in the leaves of Nicotiana benthamiana during transient expression experiments utilizing agro-infiltration. The F. graminearum FG-12 genome sequence and annotation data produced in the current study provide an extremely useful resource for both intra- and inter-species comparative analyses as well as for gene functional studies, and could greatly advance our understanding of this important plant pathogen.
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195
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Krabbenhoft TJ, MacGuigan DJ, Backenstose NJC, Waterman H, Lan T, Pelosi JA, Tan M, Sandve SR. Chromosome-Level Genome Assembly of Chinese Sucker (Myxocyprinus asiaticus) Reveals Strongly Conserved Synteny Following a Catostomid-Specific Whole-Genome Duplication. Genome Biol Evol 2021; 13:6349175. [PMID: 34383883 PMCID: PMC8412299 DOI: 10.1093/gbe/evab190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 12/27/2022] Open
Abstract
Fishes of the family Catostomidae (“suckers”; Teleostei: Cypriniformes) are hypothesized to have undergone an allopolyploidy event approximately 60 Ma. However, genomic evidence has previously been unavailable to assess this hypothesis. We sequenced and assembled the first chromosome-level catostomid genome, Chinese sucker (Myxocyprinus asiaticus), and present clear evidence of a catostomid-specific whole-genome duplication (WGD) event (“Cat-4R”). Our results reveal remarkably strong, conserved synteny since this duplication event, as well as between Myxocyprinus and an unduplicated outgroup, zebrafish (Danio rerio). Gene content and repetitive elements are also approximately evenly distributed across homeologous chromosomes, suggesting that both subgenomes retain some function, with no obvious bias in gene fractionation or subgenome dominance. The Cat-4R duplication provides another independent example of genome evolution following WGD in animals, in this case at the extreme end of conserved genome architecture over at least 25.2 Myr since the duplication. The M. asiaticus genome is a useful resource for researchers interested in understanding genome evolution following WGD in animals.
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Affiliation(s)
- Trevor J Krabbenhoft
- Department of Biological Sciences and the RENEW Institute, University at Buffalo, USA
- Corresponding author: E-mail:
| | | | | | - Hannah Waterman
- Department of Biological Sciences, University at Buffalo, USA
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, USA
- Present address: Arbor Biosciences, Ann Arbor, MI, USA
| | | | - Milton Tan
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, USA
| | - Simen R Sandve
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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196
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Huang C, Ying H, Yang X, Gao Y, Li T, Wu B, Ren M, Zhang Z, Ding J, Gao J, Wen D, Ye X, Liu L, Wang H, Sun G, Zou Y, Chen N, Wang L. The Cardamine enshiensis genome reveals whole genome duplication and insight into selenium hyperaccumulation and tolerance. Cell Discov 2021; 7:62. [PMID: 34373445 PMCID: PMC8352907 DOI: 10.1038/s41421-021-00286-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/26/2021] [Indexed: 02/05/2023] Open
Abstract
Cardamine enshiensis is a well-known selenium (Se)-hyperaccumulating plant. Se is an essential trace element associated with many health benefits. Despite its critical importance, genomic information of this species is limited. Here, we report a chromosome-level genome assembly of C. enshiensis, which consists of 443.4 Mb in 16 chromosomes with a scaffold N50 of 24 Mb. To elucidate the mechanism of Se tolerance and hyperaccumulation in C. enshiensis, we generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes. The results reveal that flavonoid, glutathione, and lignin biosynthetic pathways may play important roles in protecting C. enshiensis from stress induced by Se. Hi-C analysis of chromatin interaction patterns showed that the chromatin of C. enshiensis is partitioned into A and B compartments, and strong interactions between the two telomeres of each chromosome were correlated with histone modifications, epigenetic markers, DNA methylation, and RNA abundance. Se supplementation could affect the 3D chromatin architecture of C. enshiensis at the compartment level. Genes with compartment changes after Se treatment were involved in selenocompound metabolism, and genes in regions with topologically associated domain insulation participated in cellular responses to Se, Se binding, and flavonoid biosynthesis. This multiomics research provides molecular insight into the mechanism underlying Se tolerance and hyperaccumulation in C. enshiensis.
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Affiliation(s)
- Chuying Huang
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China. .,Hubei Selenium and Human Health Institute, Enshi, Hubei, China.
| | - Hongqin Ying
- Hubei Selenium Industrial Technology Research Institute, Enshi Autonomous Prefecture Academy of Agriculture Sciences, Enshi, Hubei, China
| | - Xibiao Yang
- Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yuan Gao
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 405 30, Gothenburg, Sweden
| | - Tuo Li
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Bo Wu
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Meng Ren
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zixiong Zhang
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Jun Ding
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Jianhua Gao
- South China Potato Research Center, Enshi Autonomous Prefecture Academy of Agricultural Sciences, Enshi, Hubei, China
| | - Dan Wen
- Bureau of Agricultural & Rural Affairs of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
| | - Xingzhi Ye
- South China Potato Research Center, Enshi Autonomous Prefecture Academy of Agricultural Sciences, Enshi, Hubei, China
| | - Ling Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei, China
| | - Huan Wang
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei, China
| | - Guogen Sun
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Yi Zou
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Nansheng Chen
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Li Wang
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
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197
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Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DW, Zeng Y, O'Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, Portwood JL, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 2021; 373:655-662. [PMID: 34353948 PMCID: PMC8733867 DOI: 10.1126/science.abg5289] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022]
Abstract
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.
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Affiliation(s)
- Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | - Margaret R Woodhouse
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | | | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Tingting Guo
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Silas Tittes
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Asher I Hudson
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | | | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Rebecca D Piri
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Na Wang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Dong Won Kim
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Amanda M Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Erin Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - John L Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Ethalinda K S Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Samantha J Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David E Hufnagel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Qiuhan Jiang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Sarah Pedersen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Michael L Syring
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Jeffrey Ross-Ibarra
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Doreen Ware
- USDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - R Kelly Dawe
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
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198
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Stuckert AMM, Chouteau M, McClure M, LaPolice TM, Linderoth T, Nielsen R, Summers K, MacManes MD. The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system. Mol Ecol 2021; 30:4039-4061. [PMID: 34145931 PMCID: PMC8457190 DOI: 10.1111/mec.16024] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/13/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022]
Abstract
A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defence, are excellent models to understand the link between vivid colour pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which multiple species share the same conspicuous phenotype can provide an even better model for understanding the mechanisms of colour production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which vivid colour and pattern are produced in a Müllerian mimicry complex of poison frogs. We did this by first assembling a high-quality de novo genome assembly for the mimic poison frog Ranitomeya imitator. This assembled genome is 6.8 Gbp in size, with a contig N50 of 300 Kbp R. imitator and two colour morphs from both Ranitomeya fantastica and R. variabilis which R. imitator mimics. We identified a large number of pigmentation and patterning genes that are differentially expressed throughout development, many of them related to melanocyte development, melanin synthesis, iridophore development and guanine synthesis. Polytypic differences within species may be the result of differences in expression and/or timing of expression, whereas convergence for colour pattern between species does not appear to be due to the same changes in gene expression. In addition, we identify the pteridine synthesis pathway (including genes such as qdpr and xdh) as a key driver of the variation in colour between morphs of these species. Finally, we hypothesize that genes in the keratin family are important for producing different structural colours within these frogs.
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Affiliation(s)
- Adam M. M. Stuckert
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Mathieu Chouteau
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA)Université de Guyane, CNRS, IFREMERCayenneFrance
| | - Melanie McClure
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA)Université de Guyane, CNRS, IFREMERCayenneFrance
| | - Troy M. LaPolice
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
| | - Tyler Linderoth
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Rasmus Nielsen
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Kyle Summers
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Matthew D. MacManes
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
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199
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Gao Z, You X, Zhang X, Chen J, Xu T, Huang Y, Lin X, Xu J, Bian C, Shi Q. A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus). Genomics 2021; 113:3349-3356. [PMID: 34343676 DOI: 10.1016/j.ygeno.2021.07.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/13/2021] [Accepted: 07/28/2021] [Indexed: 12/15/2022]
Abstract
Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.
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Affiliation(s)
- Zijian Gao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jieming Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xueqiang Lin
- BGI Marine-Hainan, BGI Marine, BGI, Wenchang 571327, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Chao Bian
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
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200
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Zhang X, Blair D, Wolinska J, Ma X, Yang W, Hu W, Yin M. Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families. Proc Biol Sci 2021; 288:20210803. [PMID: 34315260 PMCID: PMC8316793 DOI: 10.1098/rspb.2021.0803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/06/2021] [Indexed: 12/15/2022] Open
Abstract
Predation has been a major driver of the evolution of prey species, which consequently develop antipredator adaptations. However, little is known about the genetic basis underpinning the adaptation of prey to intensive predation. Here, we describe a high-quality chromosome-level genome assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of Daphnia mitsukuri, a primary forage for many fish species. Transcriptional profiling of D. mitsukuri exposed to fish kairomone revealed that this cladoceran responds to predation risk through regulating activities of Wnt signalling, cuticle pattern formation, cell cycle regulation and anti-apoptosis pathways. Genes differentially expressed in response to predation risk are more likely to be members of expanded families. Our results suggest that expansions of multiple gene families associated with chemoreception and vision allow Daphnia to enhance detection of predation risk, and that expansions of those associated with detoxification and cuticle formation allow Daphnia to mount an efficient response to perceived predation risk. This study increases our understanding of the molecular basis of prey defences, being important evolutionary adaptations playing a stabilizing role in community dynamics.
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Affiliation(s)
- Xiuping Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, People's Republic of China
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Justyna Wolinska
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Mueggelseedamm 301, 12587 Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195 Berlin, Germany
| | - Xiaolin Ma
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, People's Republic of China
| | - Wenwu Yang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, People's Republic of China
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, People's Republic of China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, People's Republic of China
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