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Moustafa K. Maize's origin to be revisited. Plant Signal Behav 2024; 19:2332017. [PMID: 38513059 PMCID: PMC10962592 DOI: 10.1080/15592324.2024.2332017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
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Han XY, Du LF, Lin ZT, Li C, Xiong T, Zhu WJ, Ye RZ, Wang N, Wang YF, Gao WY, Zhao L, Cui XM, Cao WC. Genomic characters of Anaplasma bovis and genetic diversity in China. Emerg Microbes Infect 2024; 13:2323153. [PMID: 38442029 PMCID: PMC10916922 DOI: 10.1080/22221751.2024.2323153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
The emergence of Anaplasma bovis or A. bovis-like infection in humans from China and the United States of America has raised concern about the public health importance of this pathogen. Although A. bovis has been detected in a wide range of ticks and mammals in the world, no genome of the pathogen is available up to now, which has prohibited us from better understanding the genetic basis for its pathogenicity. Here we describe an A. bovis genome from metagenomic sequencing of an infected goat in China. Anaplasma bovis had the smallest genome of the genus Anaplasma, and relatively lower GC content. Phylogenetic analysis of single-copy orthologue sequence showed that A. bovis was closely related to A. platys and A. phagocytophilum, but relatively far from intraerythrocytic Anaplasma species. Anaplasma bovis had 116 unique orthogroups and lacked 51 orthogroups in comparison to other Anaplasma species. The virulence factors of A. bovis were significantly less than those of A. phagocytophilum, suggesting less pathogenicity of A. bovis. When tested by specific PCR assays, A. bovis was detected in 23 of 29 goats, with an infection rate up to 79.3% (95% CI: 64.6% ∼94.1%). The phylogenetic analyses based on partial 16S rRNA, gltA and groEL genes indicated that A. bovis had high genetic diversity. The findings of this study lay a foundation for further understanding of the biological characteristics and genetic diversity of A. bovis, and will facilitate the formulation of prevention and control strategies.
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Affiliation(s)
- Xiao-Yu Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Li-Feng Du
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
| | - Zhe-Tao Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Cheng Li
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
| | - Tao Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Wen-Jie Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Run-Ze Ye
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
| | - Ning Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
| | - Yi-Fei Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
| | - Wan-Ying Gao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
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Li X, Li P, Tang W, Zheng J, Fan F, Jiang X, Li Z, Fang Y. Simultaneous determination of subspecies and geographic origins of 110 rice cultivars by microsatellite markers. Food Chem 2024; 445:138657. [PMID: 38354640 DOI: 10.1016/j.foodchem.2024.138657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Rice varieties of different subspecies types (indica rice and japonica rice) across various geographical origins (Hunan, Jiangsu, and Northeast China) were monitored using microsatellite markers (simple sequence repeats, SSR). 110 representative rice cultivars were collected from the main crop areas. Multiple methods including clustering analysis (neighbor-joining (NJ) method, unweighted pair-group method with arithmetic mean (UPGMA) method), principal component analysis (PCA) and model-based grouping were applied. The study revealed that 25 pairs of SSR markers exhibited a broad range of polymorphism information content (PIC) values, ranging from 0.240 to 0.830. Furthermore, our study successfully achieved a higher overall mean correct rate of 99.09% in determining the geographical origin of rice. Simultaneously, it accurately classified indica rice and japonica rice. These findings are significant as they provide an SSR fingerprint of 110 high-quality rice cultivars, serving as a valuable scientific resource for the detection of rice adulteration and traceability of its origin.
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Affiliation(s)
- Xinyue Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Peng Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Wenqian Tang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Jiayu Zheng
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Fengjiao Fan
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Xiaoyi Jiang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Ziqian Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Yong Fang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China.
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Lopes-Lima M, Geist J, Egg S, Beran L, Bikashvili A, Van Bocxlaer B, Bogan AE, Bolotov IN, Chelpanovskaya OA, Douda K, Fernandes V, Gomes-Dos-Santos A, Gonçalves DV, Gürlek ME, Johnson NA, Karaouzas I, Kebapçı Ü, Kondakov AV, Kuehn R, Lajtner J, Mumladze L, Nagel KO, Neubert E, Österling M, Pfeiffer J, Prié V, Riccardi N, Sell J, Schneider LD, Shumka S, Sîrbu I, Skujienė G, Smith CH, Sousa R, Stöckl K, Taskinen J, Teixeira A, Todorov M, Trichkova T, Urbańska M, Välilä S, Varandas S, Veríssimo J, Vikhrev IV, Woschitz G, Zając K, Zając T, Zanatta D, Zieritz A, Zogaris S, Froufe E. Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications. Mol Phylogenet Evol 2024; 195:108046. [PMID: 38447924 DOI: 10.1016/j.ympev.2024.108046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectusstat. rev., Unio gontieriistat. rev., Unio mardinensisstat. rev., Unio nanusstat. rev., and Unio vicariusstat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.
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Affiliation(s)
- M Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
| | - J Geist
- Aquatic Systems Biology, Technical University of Munich, TUM School of Life Sciences, Mühlenweg 22, 85354 Freising, Germany
| | - S Egg
- Aquatic Systems Biology, Technical University of Munich, TUM School of Life Sciences, Mühlenweg 22, 85354 Freising, Germany; Molecular Zoology, Technical University of Munich, TUM School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - L Beran
- Regional Office Kokořínsko - Máchův kraj Protected Landscape Area Administration, Nature Conservation Agency of the Czech Republic, Česká 149, CZ-27601 Mělnik, Czech Republic
| | - A Bikashvili
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - B Van Bocxlaer
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - A E Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601 USA
| | - I N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - O A Chelpanovskaya
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - K Douda
- Department of Zoology and Fisheries, FAFNR, Czech University of Life Sciences Prague, Kamýcká 129, CZ-16500 Prague, Czech Republic
| | - V Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - A Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - D V Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - M E Gürlek
- Burdur Vocational School of Food Agriculture and Livestock, Mehmet Akif Ersoy University, 15100 Burdur, Türkiye
| | - N A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - I Karaouzas
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - Ü Kebapçı
- Biology Department, Faculty of Science and Arts, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - A V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - R Kuehn
- Molecular Zoology, Technical University of Munich, TUM School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - J Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - L Mumladze
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - K-O Nagel
- Malacological Section, Senckenberg Research Institute and Natural History Museum Frankfurt/M., Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - E Neubert
- Natural History Museum, 3005 Bern, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - M Österling
- Institution of Environmental and Life Sciences, Karlstad University, Biology, 65188 Karlstad, Sweden
| | - J Pfeiffer
- National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue, Washington, DC, USA
| | - V Prié
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - N Riccardi
- CNR Water Research Institute, Largo Tonolli 50, 28922 Verbania, Italy
| | - J Sell
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - L D Schneider
- The Rural Economy and Agricultural Society, 305 96 Eldsberga, Sweden
| | - S Shumka
- Faculty Of Biotechnology and Food, Agricultural University of Tirana, Koder Kamez, Tirana 2029, Albania
| | - I Sîrbu
- Lucian Blaga University of Sibiu, Faculty of Sciences, 5-7 Dr. I. Rațiu St., 550012 Sibiu, Romania
| | - G Skujienė
- Department of Zoology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10223 Vilnius, Lithuania
| | - C H Smith
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - R Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - K Stöckl
- Bavarian Academy for Nature Conservation and Landscape Management, Seethalerstrasse 6, 83410 Laufen, Germany
| | - J Taskinen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - A Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - M Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - T Trichkova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - M Urbańska
- Department of Zoology, Poznań University of Life Sciences, ul. Wojska Polskiego 28, 60-637 Poznań, Poland
| | - S Välilä
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - S Varandas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; CITAB-UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, Vila Real, Portugal
| | - J Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - I V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - G Woschitz
- IFIS - Ichthyological Research Initiative Styria, 1160 Vienna, Austria
| | - K Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - T Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - D Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - A Zieritz
- School of Geography, University of Nottingham, University Park, Sir Clive Granger Building, Nottingham NG7 2RD, United Kingdom
| | - S Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - E Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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Paul KMM, Simpson SV, Nundu SS, Arima H, Yamamoto T. Genetic diversity of glutamate-rich protein (GLURP) in Plasmodium falciparum isolates from school-age children in Kinshasa, DRC. Parasitol Int 2024; 100:102866. [PMID: 38350548 DOI: 10.1016/j.parint.2024.102866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/15/2024]
Abstract
Malaria infections in school-age children further make it difficult to control the disease's spread. Moreover, the genetic diversity of glutamate-rich protein, potentially a candidate for vaccine development, has not yet been investigated in the Democratic Republic of Congo. Therefore, we aimed to assess the genetic diversity of the immunodominant C-terminal repetitive region (R2) of Plasmodium falciparum glutamate-rich protein gene (pfglurp) among school-age children living in Kinshasa, DRC. We conducted nested PCR targeting R2 of pfglurp and the amplicon were directly sequenced. We summarized the prevalence of mutations of bases and amino acids and indicated the amino acid repeat sequence in the R2 region by the unit code. We then statistically analyzed whether there was a relationship between the number of mutations in the pfglurp gene and attributes. In 221 samples, haplotype 1 was the most common (n = 137, 61.99%), with the same sequence as the 3D7 strain. Regarding the number of base mutations, it was higher in urban areas than rural areas (p = 0.0363). When genetic neutrality was tested using data from 171 samples of the single strain, Tajima's D was -1.857 (p = 0.0059). In addition, FST as the genetic distance between all attributes was very small and no significant difference was observed. This study clarified the genetic mutation status and relevant patient attributes among School-age children in the DRC. We found that urban areas are more likely to harbour pfglurp mutations. Future research needs to clarify the reason and mechanism involved.
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Affiliation(s)
- Kambale Mathe Mowa Paul
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Nagasaki University, Nagasaki, Japan
| | - Shirley V Simpson
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Nagasaki University, Nagasaki, Japan
| | - Sabin S Nundu
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | - Hiroaki Arima
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.
| | - Taro Yamamoto
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Nagasaki University, Nagasaki, Japan
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Sun X, Pan Q, Hubley B, Ye Z, Zhang P, Xie Q. Geomorphic impacts within Red River Fault and island shifting as witnessed by the phylogeography of the largest water strider. Mol Phylogenet Evol 2024; 195:108062. [PMID: 38485104 DOI: 10.1016/j.ympev.2024.108062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/16/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Palaeogeological events and climate oscillations profoundly impact the demographics and distributions of small-range species, increasing the extinction risk. The largest water strider worldwide, Gigantometra gigas (Hemiptera: Gerridae), exhibits restricted distributions in Vietnam and southern China. Herein, we generated three genomic datasets (mitogenomes, 146 nuclear protein-coding genes and single nucleotide polymorphisms) with ecological niche modelling (ENM) to explicitly test whether the present-day distribution of G. gigas actually resulted from geographical and climatic effects. We found that the origin of this largest water strider reached the divergence time of the genus within Gerridae, providing a greater opportunity to explore its response to geographic movements. The right-lateral motion of the Red River Fault facilitated the divergence of two phylogeographic lineages, resulting in the "north-south component" genetic pattern in G. gigas. The Hainan and southeast Vietnam populations of the southern linage were completely separated by the Beibu Gulf but exhibited similar genetic compositions, confirming that Hainan had a continental origin and that Hainan Island joined with the Indo-China Peninsula to promote gene exchange among populations. Additionally, we noticed the low genetic diversity but long demographic history of the northern lineage, which displayed population dynamics opposite to those of other organisms. Integrating the demographic changes and ENM findings revealed that suitable habitat contraction and rapid demographic decline during the Last Glacial Maximum (LGM) triggered the low genetic diversity of the northern lineage. Overall, the demographic history of the largest water strider was mainly shaped by geographical features, and first provided evidence from the phylogeographic perspective of aquatic insects to support the hypothesis of Hainan Island shifting.
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Affiliation(s)
- Xiaoya Sun
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity & Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China.
| | - Qiqi Pan
- School of Life Sciences, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Brad Hubley
- Natural History - Entomology Royal Ontario Museum, 100 Queen's Park, Toronto, Canada
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China.
| | - Peng Zhang
- School of Life Sciences, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Qiang Xie
- School of Life Sciences, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, China
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Thaker P, Mahajan N, Mukherjee MB, Colah RB. Wide spectrum of novel and rare hemoglobin variants in the multi-ethnic Indian population: A review. Int J Lab Hematol 2024; 46:434-450. [PMID: 38504512 DOI: 10.1111/ijlh.14267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
The hemoglobin (Hb) variants are qualitative abnormalities due to production of structurally abnormal globin proteins. They are categorized based on the type of mutation present in the α1, α2, β, Gγ, Aγ and δ globin genes. So far, more than 1550 Hb variants are reported in the database. They could lead to Hb polymerization, Hb instability, altered oxygen affinity and decreased oxygen-carrying capacity of Hb or have no clinical manifestations. In India, ethnic diversity, consanguinity, regional variations and migration result in the presence of different Hb variants. We have compiled all the variants of α, β and δ globin chains in heterozygous, homozygous and in compound heterozygous forms reported from India in the last 52 years. Of the 63 rare and novel hemoglobin variants reported from India, 22 were α-globin chain variants, 37 were β-globin chain variants and 4 were δ-globin chain variants. Twelve novel Hb variants (Hb J Rajappan, Hb Koya Dora, Hb Rampa, Hb Godavari, Hb Chandigarh, Hb D Agri, Hb Lucknow, Hb Vellore, Hb Midnapore, Hb Bijnor, Hb A2Tianhe and Hb A2Saurashtra) were identified among persons of Indian origin. Majority of them were picked up on HPLC. Some of the variants like Hb Titusville, Hb Shimonoseki, Hb Chandigarh, Hb D Agri, Hb Yaizu and Hb Vellore eluted in the HbS window whereas variants like HbD Iran, Hb St. Louis, Hb G Coushata, HbM Saskatoon, Hb Lucknow, Hb Grange-Blanche and Hb Tianshui showed falsely elevated HbA2. Hence, careful and systematic investigations are required to identify them.
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Affiliation(s)
- Pallavi Thaker
- Department of Haematogenetics, Indian Council of Medical Research-National Institute of Immunohaematology (ICMR-NIIH), Mumbai, India
| | - Namrata Mahajan
- Department of Haematogenetics, Indian Council of Medical Research-National Institute of Immunohaematology (ICMR-NIIH), Mumbai, India
| | - Malay B Mukherjee
- Department of Haematogenetics, Indian Council of Medical Research-National Institute of Immunohaematology (ICMR-NIIH), Mumbai, India
| | - Roshan B Colah
- Department of Haematogenetics, Indian Council of Medical Research-National Institute of Immunohaematology (ICMR-NIIH), Mumbai, India
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Le VN, Le VNB, Hoang XS, Le VD. Distribution of human papillomavirus among Vietnamese women with cervical cancer and unusual genetic variability of HPV16. Virology 2024; 594:110058. [PMID: 38520797 DOI: 10.1016/j.virol.2024.110058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/21/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
HPV16, with typical mutations that differ in geographical distribution and carcinogenic potency, has implications for cervical cancer screening, clinical diagnosis, and treatment. DNASTAR and MEGA were used to identify HPV16 variants and construct a phylogenetic tree. The most prevalent HPV genotypes were HPV16 (63.9%), HPV18 (26.7%), and other HPV (6.9%). HPV16 alterations were found in all E6, E7, and L1 genes, including 15 missense and 18 synonymous mutations. Missense mutations include R10G, Q14H, D25E, H78Y, L83V (E6); M29V, R35K, L78R, L95P (E7); H73Y, T176 N, N178T, T317P, T386S, L472F/I (L1). HPV16 sublineages include A1 (17.2%), A2 (0.9%), A3 (56.0%), A4 (19.0%), D1 (4.3%), and D3 (2.6%). Although several mutations in the oncoproteins E6, E7, and L1 have been detected, mutations known to be associated with cervical cancer risk, such as D25E and L83V, occur at a relatively low frequency. This suggests that HPV16 mutations are associated with cervical cancer through a complicated mechanism.
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Affiliation(s)
- Van Nam Le
- Departments of Infectious Disease, Military Hospital 103, 261 Phung Hung, Ha Dong, Hanoi, Viet Nam
| | - Van Nguyen Bang Le
- Luong the Vinh High School, 35 Dinh Nup, Trung Hoa, Cau Giay, Hanoi, Viet Nam
| | - Xuan Son Hoang
- Departments of Obstetrics and Gynecology, Cho Moi District General Hospital, Na Mo Village, Dong Tam Town, Cho Moi District, Bac Kan Province, Viet Nam
| | - Van Duyet Le
- Micobiology and Moclecular Biology Department, National Hospital for Tropical Diseases, 78 Giai Phong, Dong Da, Hanoi, Viet Nam.
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Wang S, Li Y, Jiang K, Zhou J, Chen J, Liang J, Ndoni A, Xue H, Ye Z, Bu W. Identifying a potentially invasive population in the native range of a species: The enlightenment from the phylogeography of the yellow spotted stink bug, Erthesina fullo (Hemiptera: Pentatomidae). Mol Phylogenet Evol 2024; 195:108056. [PMID: 38493987 DOI: 10.1016/j.ympev.2024.108056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/15/2024] [Accepted: 03/09/2024] [Indexed: 03/19/2024]
Abstract
The yellow spotted stink bug (YSSB), Erthesina fullo (Thunberg, 1783) is an important Asian pest that has recently successfully invaded Europe and an excellent material for research on the initial stage of biological invasion. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of YSSB for the first time based on population genetic methods [using double digest restriction-site associated DNA (ddRAD) data and mitochondrial COI and CYTB] and ecological niche modelling. The results showed that four lineages (east, west, southwest, and Hainan Island) were established in the native range with a strong east-west differentiation phylogeographical structure, and the violent climate fluctuation might cause population divergence during the Middle and Upper Pleistocene. In addition, land bridges and monsoon promote dispersal and directional genetic exchanging between island populations and neighboring continental populations. The east lineage (EA) was identified as the source of invasion in Albania. EA had the widest geographical distribution among all other lineages, with a star-like haplotype network with the main haplotype as the core. It also had a rapid population expansion history, indicating that the source lineage might have stronger diffusion ability and adaptability. Our findings provided a significant biological basis for fine tracking of invasive source at the lineage or population level and promote early invasion warning of potential invasive species on a much subtler lineage level.
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Affiliation(s)
- Shujing Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Yanfei Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Kun Jiang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, PR China
| | - Jiayue Zhou
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Juhong Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Jingyu Liang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | | | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
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10
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Fu S, Chen X, Wang K, Chen J, Zhou J, Yi W, Lyu M, Ye Z, Bu W. Shared phylogeographic patterns and environmental responses of co-distributed soybean pests: Insights from comparative phylogeographic studies of Riptortus pedestris and Riptortus linearis in the subtropics of East Asia. Mol Phylogenet Evol 2024; 195:108055. [PMID: 38485106 DOI: 10.1016/j.ympev.2024.108055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/31/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
Comparative phylogeographic studies of closely related species sharing co-distribution areas can elucidate the role of shared historical factors and environmental changes in shaping their phylogeographic pattern. The bean bugs, Riptortus pedestris and Riptortus linearis, which both inhabit subtropical regions in East Asia, are recognized as highly destructive soybean pests. Many previous studies have investigated the biological characteristics, pheromones, chemicals and control mechanisms of these two pests, but few studies have explored their phylogeographic patterns and underlying factors. In this study, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) dataset to investigate phylogeographic patterns and construct ecological niche models (ENM) for both Riptortus species. Our findings revealed similar niche occupancies and population genetic structures between the two species, with each comprising two phylogeographic lineages (i.e., the mainland China and the Indochina Peninsula clades) that diverged approximately 0.1 and 0.3 million years ago, respectively. This divergence likely resulted from the combined effects of temperatures variation and geographical barriers in the mountainous regions of Southwest China. Further demographic history and ENM analyses suggested that both pests underwent rapid expansion prior to the Last Glacial Maximum (LGM). Furthermore, ENM predicts a northward shift of both pests into new soybean-producing regions due to global warming. Our study indicated that co-distribution soybean pests with overlapping ecological niches and similar life histories in subtropical regions of East Asia exhibit congruent phylogeographic and demographic patterns in response to shared historical biogeographic drivers.
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Affiliation(s)
- Siying Fu
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xin Chen
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China(2)
| | - Kaibin Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Juhong Chen
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiayue Zhou
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wenbo Yi
- Department of Biology, Xinzhou Normal University, Xinzhou, Shanxi, China(2)
| | - Minhua Lyu
- Nanchang University, Affiliated Hospital 1, Jiangxi, China(2)
| | - Zhen Ye
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin 300071, China.
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11
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Boulanger L, Planchon C, Taudière A, McCoy KD, Burgess STG, Nisbet AJ, Bartley K, Galliot P, Creach P, Sleeckx N, Roy L. The Poultry Red Mite, Dermanyssus gallinae, travels far but not frequently, and takes up permanent residence on farms. Infect Genet Evol 2024; 120:105584. [PMID: 38521481 DOI: 10.1016/j.meegid.2024.105584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
Management of Dermanyssus gallinae, a cosmopolitan hematophagous mite responsible for damage in layer poultry farming, is hampered by a lack of knowledge of its spatio-temporal population dynamics. Previous studies have shown that the circulation of this pest between farms is of strictly anthropogenic origin, that a mitochondrial haplogroup has been expanding on European farms since the beginning of the 21st century and that its local population growth may be particularly rapid. To refine our understanding of how D. gallinae spreads within and among farms, we characterized the genetic structure of mite populations at different spatial scales and sought to identify the main factors interrupting gene flow between poultry houses and between mitochondrial haplogroups. To this end, we selected and validated the first set of nuclear microsatellite markers for D. gallinae and sequenced a region of the CO1-encoding mitochondrial gene in a subsample of microsatellite-genotyped mites. We also tested certain conditions required for effective contamination of a poultry house through field experimentation, and conducted a survey of practices during poultry transfers. Our results confirm the role of poultry transport in the dissemination of mite populations, but the frequency of effective contamination after the introduction of contaminated material into poultry houses seems lower than expected. The high persistence of mites on farms, even during periods when poultry houses are empty and cleaned, and the very large number of nodes in the logistic network (large number of companies supplying pullets or transporting animals) undoubtedly explain the very high prevalence on farms. Substantial genetic diversity was measured in farm populations, probably as a result of the mite's known haplodiploid mode of sexual reproduction, coupled with the dense logistic network. The possibility of the occasional occurrence of asexual reproduction in this sexually reproducing mite was also revealed in our analyses, which could explain the extreme aggressiveness of its demographic dynamics under certain conditions.
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Affiliation(s)
- L Boulanger
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919 route de Mende, 3400 Montpellier, France
| | - C Planchon
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919 route de Mende, 3400 Montpellier, France
| | - A Taudière
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919 route de Mende, 3400 Montpellier, France
| | - K D McCoy
- Université de Montpellier, CNRS, IRD, MIVEGEC, Domaine La Valette - 900, rue Jean François BRETON, 34090 Montpellier, France
| | - S T G Burgess
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ, UK
| | - A J Nisbet
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ, UK
| | - K Bartley
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ, UK
| | - P Galliot
- Institut Technique de l'AVIculture (ITAVI), FranceITAVI, 41 rue Beaucemaine, 22440 Ploufragan, France
| | - P Creach
- Institut Technique de l'AVIculture (ITAVI), FranceITAVI, 41 rue Beaucemaine, 22440 Ploufragan, France
| | - N Sleeckx
- Experimental Poultry Centre, 77 Poiel, Geel 2440, Belgium
| | - Lise Roy
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919 route de Mende, 3400 Montpellier, France.
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Alanazi AE, Alhumaidy AA, Almutairi H, Awadalla ME, Alkathiri A, Alarjani M, Aldawsari MA, Maniah K, Alahmadi RM, Alanazi BS, Eifan S, Alosaimi B. Evolutionary analysis of LMP-1 genetic diversity in EBV-associated nasopharyngeal carcinoma: Bioinformatic insights into oncogenic potential. Infect Genet Evol 2024; 120:105586. [PMID: 38508363 DOI: 10.1016/j.meegid.2024.105586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
EBV latent membrane protein 1 (LMP-1) is an important oncogene involved in the induction and maintenance of EBV infection and the activation of several cell survival and proliferative pathways. The genetic diversity of LMP-1 has an important role in immunogenicity and tumorigenicity allowing escape from host cell immunity and more metastatic potential of LMP-1 variants. This study explored the evolutionary of LMP-1 in EBV-infected patients at an advanced stage of nasopharyngeal carcinoma (NPC). Detection of genetic variability in LMP-1 genes was carried out using Sanger sequencing. Bioinformatic analysis was conducted for translation and nucleotide alignment. Phylogenetic analysis was used to construct a Bayesian tree for a deeper understanding of the genetic relationships, evolutionary connections, and variations between sequences. Genetic characterization of LMP-1 in NPC patients revealed the detection of polymorphism in LMP-1 Sequences. Motifs were identified within three critical LMP-1 domains, such as PQQAT within CTAR1 and YYD within CTAR2. The presence of the JACK3 region at specific sites within CTAR3, as well as repeat regions at positions (122-132) and (133-143) within CTAR3, was also annotated. Additionally, several mutations were detected including 30 and 69 bp deletions, 33 bp repeats, and 15 bp insertion. Although LMP-1 strains appear to be genetically diverse, they are closely related to 3 reference strains: prototype B95.8, Med- 30 bp deletion, and Med + 30 bp deletion. In our study, one of the strains harboring the 30 bp deletion had both bone and bone marrow metastasis which could be attributed to the fact that LMP-1 is involved in tumor metastasis, evasion and migration of NPC cells. This study provided valuable insights into genetic variability in LMP-1 sequences of EBV in NPC patients. Further functional studies would provide a more comprehensive understanding of the molecular characteristics, epidemiology, and clinical implications of LMP-1 polymorphisms in EBV-related malignancies.
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Affiliation(s)
- Abdullah E Alanazi
- Comprehensive Cancer Center, King Fahad Medical City, Riyadh Second Health Cluster, Riyadh 11525, Saudi Arabia
| | | | - Hatim Almutairi
- Bioinformatics Laboratory, Public Health Authority, Riyadh 11451, Saudi Arabia
| | - Maaweya E Awadalla
- Research Center, King Fahad Medical City, Riyadh Second Heath Cluster, Riyadh 11525, Saudi Arabia
| | - Abdulrahman Alkathiri
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Modhi Alarjani
- Research Center, King Fahad Medical City, Riyadh Second Heath Cluster, Riyadh 11525, Saudi Arabia
| | - Mesfer Abdullah Aldawsari
- Department of Health Education, Alyamamah Hospital, Riyadh Second Heath Cluster, Riyadh 11525, Saudi Arabia
| | - Khalid Maniah
- Department of Biology, King Khalid Military Academy, Riyadh 22140, Saudi Arabia
| | - Reham M Alahmadi
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Bader S Alanazi
- Research Center, King Fahad Medical City, Riyadh Second Heath Cluster, Riyadh 11525, Saudi Arabia
| | - Saleh Eifan
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Bandar Alosaimi
- Research Center, King Fahad Medical City, Riyadh Second Heath Cluster, Riyadh 11525, Saudi Arabia.
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13
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Simon SJ, Furches A, Chhetri H, Evans L, Abeyratne CR, Jones P, Wimp G, Macaya-Sanz D, Jacobson D, Tschaplinski TJ, Tuskan GA, DiFazio SP. Genetic underpinnings of arthropod community distributions in Populus trichocarpa. New Phytol 2024; 242:1307-1323. [PMID: 38488269 DOI: 10.1111/nph.19660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/21/2024] [Indexed: 04/12/2024]
Abstract
Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.
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Affiliation(s)
- Sandra J Simon
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Anna Furches
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Hari Chhetri
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
- Computational Systems Biology Group, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Luke Evans
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, 80309, USA
| | | | - Piet Jones
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Gina Wimp
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Daniel Jacobson
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Timothy J Tschaplinski
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gerald A Tuskan
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
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14
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Hutchins M, Douglas T, Pollack L, Saltz JB. Genetic Variation in Male Aggression Is Influenced by Genotype of Prior Social Partners in Drosophila melanogaster. Am Nat 2024; 203:551-561. [PMID: 38635366 DOI: 10.1086/729463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
AbstractSocial behaviors can be influenced by the genotypes of interacting individuals through indirect genetic effects (IGEs) and can also display developmental plasticity. We investigated how developmental IGEs, which describe the effects of a prior social partner's genotype on later behavior, can influence aggression in male Drosophila melanogaster. We predicted that developmental IGEs cannot be estimated by simply extending the effects of contextual IGEs over time and instead have their own unique effects on behavior. On day 1 of the experiment, we measured aggressive behavior in 15 genotypic pairings (n = 600 males). On day 2, each of the males was paired with a new opponent, and aggressive behavior was again measured. We found contextual IGEs on day 1 of the experiment and developmental IGEs on day 2 of the experiment: the influence of the day 1 partner's genotype on the focal individual's day 2 behavior depended on the genotypic identity of both the day 1 partner and the focal male. Importantly, the developmental IGEs in our system produced fundamentally different dynamics than the contextual IGEs, as the presence of IGEs was altered over time. These findings represent some of the first empirical evidence demonstrating developmental IGEs, a first step toward incorporating developmental IGEs into our understanding of behavioral evolution.
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15
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Aguilar P, Pérez I de Lanuza G, Carneiro M, Andrade P, Pinho C. The role of historical biogeography in shaping colour morph diversity in the common wall lizard. Mol Ecol 2024; 33:e17338. [PMID: 38572696 DOI: 10.1111/mec.17338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
The maintenance of polymorphisms often depends on multiple selective forces, but less is known on the role of stochastic or historical processes in maintaining variation. The common wall lizard (Podarcis muralis) is a colour polymorphic species in which local colour morph frequencies are thought to be modulated by natural and sexual selection. Here, we used genome-wide single-nucleotide polymorphism data to investigate the relationships between morph composition and population biogeography at a regional scale, by comparing morph composition with patterns of genetic variation of 54 populations sampled across the Pyrenees. We found that genetic divergence was explained by geographic distance but not by environmental features. Differences in morph composition were associated with genetic and environmental differentiation, as well as differences in sex ratio. Thus, variation in colour morph frequencies could have arisen via historical events and/or differences in the permeability to gene flow, possibly shaped by the complex topography and environment. In agreement with this hypothesis, colour morph diversity was positively correlated with genetic diversity and rates of gene flow and inversely correlated with the likelihood of the occurrence of bottlenecks. Concurrently, we did not find conclusive evidence for selection in the two colour loci. As an illustration of these effects, we observed that populations with higher proportions of the rarer yellow and yellow-orange morphs had higher genetic diversity. Our results suggest that processes involving a decay in overall genetic diversity, such as reduced gene flow and/or bottleneck events have an important role in shaping population-specific morph composition via non-selective processes.
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Affiliation(s)
- Prem Aguilar
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Guillem Pérez I de Lanuza
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Ethology Lab, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Miguel Carneiro
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pedro Andrade
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Catarina Pinho
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Kazilas C, Dufresnes C, France J, Kalaentzis K, Martínez-Solano I, de Visser MC, Arntzen JW, Wielstra B. Spatial genetic structure in European marbled newts revealed with target enrichment by sequence capture. Mol Phylogenet Evol 2024; 194:108043. [PMID: 38382821 DOI: 10.1016/j.ympev.2024.108043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/21/2023] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
European marbled newts come in two species that have abutting ranges. The northern species, Triturus marmoratus, is found in France and the northern part of the Iberian Peninsula, whereas the southern species, T. pygmaeus, is found in the southwestern corner of the Iberian Peninsula. We study the intraspecific genetic differentiation of the group because morphological data show geographical variation and because the Iberian Peninsula is a recognized center of speciation and intraspecific genetic diversity for all kinds of organisms, amphibians included. We use target enrichment by sequence capture to generate c. 7 k nuclear DNA markers. We observe limited genetic exchange between the species, which confirms their distinctiveness. Both species show substantial genetic structuring that is only in part mirrored by morphological variation. Genetically differentiated groups are found in the south (T. marmoratus) and west (T. pygmaeus) of the species ranges. Our observations highlight the position of the Iberian Peninsula as a hotspot for genetic differentiation.
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Affiliation(s)
- Christos Kazilas
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands.
| | - Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China; Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - James France
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Konstantinos Kalaentzis
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Iñigo Martínez-Solano
- Museo Nacional de Ciencias Naturales, MNCN-CSIC, c/ José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Manon C de Visser
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
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Jitsamai W, Kamkong P, Traub RJ, Taweethavonsawat P. New insight into genetic diversity of zoonotic-potential Ancylostoma ceylanicum in stray cats living in Bangkok, Thailand, based on deep amplicon sequencing. Zoonoses Public Health 2024; 71:236-247. [PMID: 38053474 DOI: 10.1111/zph.13102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/25/2023] [Accepted: 11/25/2023] [Indexed: 12/07/2023]
Abstract
AIMS This study aimed to characterize feline hookworms from stray cats living in Bangkok. METHODS AND RESULTS A total of 56 hookworm-positive faecal samples were identified for hookworm species by using PCR targeting the ITS1, 5.8S, and ITS2 fragment and qPCR targeting ITS2. Of 56 samples, 96.4% (54/56) were identified as Ancylostoma ceylanicum and 1.8% (1/56) as Ancylostoma caninum. With qPCR, 89.3% (50/56) were identified as single A. ceylanicum infection and 5.4% (3/56) as coinfection of A. ceylanicum and A. caninum. For genetic characterization of A. ceylanicum, 10 samples were pooled, and the partial COI gene was amplified, followed by deep amplicon sequencing. Five pooled samples were analysed, and 99.73% were identified with A. ceylanicum sequences, which were allocated into 19 haplotypes (AC01-AC19). Genetic diversity findings for A. ceylanicum in Asia revealed that three of eight haplotypes considered of zoonotic significance occurred in humans, dogs, and cats, including haplotypes H01, H20, and H21. The predominant haplotype in this study, AC01, was clustered with H01-a zoonotic haplotype. CONCLUSIONS The diversity obtained by deep amplicon sequencing supported that the A. ceylanicum community had high genetic variation. Deep amplicon sequencing was a useful method to determine source, zoonotic potential, and host-parasite relationship.
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Affiliation(s)
- Wanarit Jitsamai
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Patchana Kamkong
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Rebecca J Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Piyanan Taweethavonsawat
- Parasitology Unit, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Biomarkers in Animal Parasitology Research Group, Chulalongkorn University, Bangkok, Thailand
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18
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Yan WL, Li XM, Qin SY, Xue NY, Zou Y, Li JH, Zhang XX, Ni HB. Subtypes of Blastocystis in Tibetan Antelope (Pantholops hodgsonii). Res Vet Sci 2024; 171:105233. [PMID: 38520840 DOI: 10.1016/j.rvsc.2024.105233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
Blastocystis is a protist that is distributed in the gut tract of humans and animals. However, the reports about Blastocystis infection in Tibetan antelope are scarce. We collected 173 Tibetan antelope feces samples from Xinjiang, Qinghai and Xizang, and amplified the SSU rRNA gene of 600 bp region of Blastocystis in our research. Fifty-one samples in total were positive for Blastocystis, with all subtypes being ST31. The lowest prevalence of Blastocystis was observed in Xizang (2/20, 9.1%), followed by Qinghai (18/92, 16.4%), Xinjiang (31/61, 33.7%). The highest prevalence of Blastocystis in Tibetan antelope was detected during the summer was (19/30, 38.8%). This is the first research work regarding the Blastocystis subtypes ST31 in Tibetan antelope. Our research provides information for future researches on the distribution of this Blastocystis subtype and the control of Blastocystis infection.
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Affiliation(s)
- Wei-Lan Yan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, PR China
| | - Xiao-Man Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, PR China
| | - Si-Yuan Qin
- Center of Prevention and Control Biological Disaster, State Forestry and Grassland Administration, Shenyang, Liaoning Province 110034, PR China; Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin Province, PR China
| | - Nian-Yu Xue
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China
| | - Yang Zou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Jing-Hao Li
- Center of Prevention and Control Biological Disaster, State Forestry and Grassland Administration, Shenyang, Liaoning Province 110034, PR China
| | - Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, PR China
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, PR China.
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19
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Sun Y, Nan H, Zhang C, Yang X, Zhao Y, Feng G, Ma L. Genetic characteristics of Blastocystis sp. in cattle from Hebei Province, China. Microb Pathog 2024; 190:106629. [PMID: 38522492 DOI: 10.1016/j.micpath.2024.106629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Blastocystis sp. is a protozoan parasite that infects the intestines of humans and animals, causing chronic diseases such as skin rashes, abdominal pain, and irritable bowel syndrome. A survey was conducted to determine the prevalence and genetic diversity of Blastocystis sp. infection in cattle, in Hebei Province, China. 2746 cattle fecal samples were collected from 11 cities in Hebei Province and analyzed using polymerase chain reaction targeting the Blastocystis sp. barcoding gene. MEGA, PhyloSuite, and PopART were used to analyze the subtype, sequence signature, pairwise genetic distance, and genetic diversity indices. The results showed that the Blastocystis sp. detection rate was 12.60% (346/2746). The infection rate in different herds was affected by region, age, breeding mode, and variety; that is, the infection rates in areas of southern Hebei, cattle under one year old, intensive raising, and dairy cattle were higher than the infection rates in northern Hebei, cattle over one year old, scatter feeding, and beef cattle. Seven Blastocystis subtypes were identified, namely, ST1, ST2, ST5, ST10, ST14, ST21, and ST26; ST10 was the dominant subtype, and ST14 was the second most common subtype. A total of 374 polymorphic and conserved sites were obtained, including 273 invariable (monomorphic) sites and 101 variable (polymorphic) sites, accounting for 27.01% of all nucleotides. The nucleotide diversity index (Pi) was 0.07749, and the haplotype (gene) diversity index (Hd) was 0.946. This study provides the first comprehensive information on the epidemiological situation of Blastocystis sp. infection in cattle from Hebei Province, China, and revealed rich genetic diversity of Blastocystis sp.
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Affiliation(s)
- Yuxin Sun
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Huizhu Nan
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Chao Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xin Yang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yan Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Gang Feng
- Tangshan Municipal Administration Center of Zoo, Tangshan, 063000, China
| | - Lei Ma
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
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20
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Hagenbuch F, Loehrer S, Marti H, Kasimov V, Jelocnik M, Borel N. Investigation of Chlamydia pecorum in livestock from Switzerland reveals a high degree of diversity in bovine strains. Vet Microbiol 2024; 292:110057. [PMID: 38502978 DOI: 10.1016/j.vetmic.2024.110057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Chlamydia pecorum is a widespread veterinary chlamydial species causing endemic infections in livestock, such as ruminants and pigs, globally. However, there is limited contemporary knowledge on infecting strain diversity in various hosts. This study aimed to evaluate the genetic diversity of C. pecorum strains infecting Swiss livestock through C. pecorum genotyping and phylogenetic analyses in comparison to the global population, while also assessing chlamydial strains for plasmid carriage. A total of 263 C. pecorum positive samples from clinically healthy ruminant and pig herds (Bovines = 216, sheep = 25, pigs = 14) as well as placentae from eight C. pecorum positive ruminant abortion cases from other Swiss herds were investigated. The ompA and Multi-Locus sequence typing revealed novel C. pecorum genotypes, and bovine strains exhibited considerable genetic diversity, contrasting with lower diversity in sheep and pig strains. C. pecorum plasmid was detected in 100.0% of sheep (41/41) and pig (255/255) samples, and in 69.4% of bovine samples (150/216). In contrast, no plasmid was detected in the eight C. pecorum-positive ruminant abortion cases either representing plasmid-less strains or possibly escaping PCR detection due to autolysis of the placenta. This study supports the genetic diversity of C. pecorum strains, particularly in bovines, and identifies novel sequence types in Swiss livestock.
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Affiliation(s)
- Fabian Hagenbuch
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Samuel Loehrer
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Hanna Marti
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Vasilli Kasimov
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia; Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, 4556, Australia
| | - Martina Jelocnik
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia; Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, 4556, Australia
| | - Nicole Borel
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich 8057, Switzerland.
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21
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Amjadi M, Hayatmehr Z, Egyed B, Tavallaei M, Szécsényi-Nagy A. A comprehensive review of HVS-I mitochondrial DNA variation of 19 Iranian populations. Ann Hum Genet 2024; 88:259-277. [PMID: 38161274 DOI: 10.1111/ahg.12544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
Iran is located along the Central Asian corridor, a natural artery that has served as a cross-continental route since the first anatomically modern human populations migrated out of Africa. We compiled and reanalyzed the HVS-I (hypervariable segment-I) of 3840 mitochondrial DNA (mtDNA) sequences from 19 Iranian populations and from 26 groups from adjacent countries to give a comprehensive review of the maternal genetic variation and investigate the impact of historical events and cultural factors on the maternal genetic structure of modern Iranians. We conclude that Iranians have a high level of genetic diversity. Thirty-six haplogroups were observed in Iran's populations, and most of them belong to widespread West-Eurasian haplogroups, such as H, HV, J, N, T, and U. In contrast, the predominant haplogroups observed in most of the adjacent countries studied here are H, M, D, R, U, and C haplogroups. Using principal component analysis, clustering, and genetic distance-based calculations, we estimated moderate genetic relationships between Iranian and other Eurasian groups. Further, analyses of molecular variance and comparing geographic and genetic structures indicate that mtDNA HVS-I sequence diversity does not exhibit any sharp geographic structure in the country. Barring a few from some culturally distinct and naturally separated minorities, most Iranian populations have a homogenous maternal genetic structure.
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Affiliation(s)
- Motahareh Amjadi
- Department of Genetics, ELTE Doctoral School of Biology, Eötvös Loránd University, Budapest, Hungary
- HUN-REN Research Centre for the Humanities, Institute of Archaeogenomics, Budapest, Hungary
| | - Zahra Hayatmehr
- Faculty of Management and Financial Science, Department of Management, Khatam University, Tehran, Iran
| | - Balázs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | | | - Anna Szécsényi-Nagy
- HUN-REN Research Centre for the Humanities, Institute of Archaeogenomics, Budapest, Hungary
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22
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Nilson SM, Burke JM, Murdoch BM, Morgan JLM, Lewis RM. Pedigree diversity and implications for genetic selection of Katahdin sheep. J Anim Breed Genet 2024; 141:304-316. [PMID: 38108572 DOI: 10.1111/jbg.12842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023]
Abstract
The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (Ne) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the Ne is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current Ne suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.
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Affiliation(s)
- Sara M Nilson
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Joan M Burke
- USDA, ARS, Dale Bumpers Small Farms Research Center, Booneville, Arkansas, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, USA
| | | | - Ronald M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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23
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Rohner PT, Moczek AP. Vertically inherited microbiota and environment modifying behaviours conceal genetic variation in dung beetle life history. Proc Biol Sci 2024; 291:20240122. [PMID: 38628120 PMCID: PMC11021930 DOI: 10.1098/rspb.2024.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/15/2024] [Indexed: 04/19/2024] Open
Abstract
Diverse organisms actively manipulate their (sym)biotic and physical environment in ways that feed back on their own development. However, the degree to which these processes affect microevolution remains poorly understood. The gazelle dung beetle both physically modifies its ontogenetic environment and structures its biotic interactions through vertical symbiont transmission. By experimentally eliminating (i) physical environmental modifications and (ii) the vertical inheritance of microbes, we assess how environment modifying behaviour and microbiome transmission shape heritable variation and evolutionary potential. We found that depriving larvae of symbionts and environment modifying behaviours increased additive genetic variance and heritability for development time but not body size. This suggests that larvae's ability to manipulate their environment has the potential to modify heritable variation and to facilitate the accumulation of cryptic genetic variation. This cryptic variation may become released and selectable when organisms encounter environments that are less amenable to organismal manipulation or restructuring. Our findings also suggest that intact microbiomes, which are commonly thought to increase genetic variation of their hosts, may instead reduce and conceal heritable variation. More broadly, our findings highlight that the ability of organisms to actively manipulate their environment may affect the potential of populations to evolve when encountering novel, stressful conditions.
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Affiliation(s)
- Patrick T. Rohner
- Department of Ecology, Behavior, and Evolution, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Armin P. Moczek
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
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24
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Stringer EJ, Gruber B, Sarre SD, Wardle GM, Edwards SV, Dickman CR, Greenville AC, Duncan RP. Boom-bust population dynamics drive rapid genetic change. Proc Natl Acad Sci U S A 2024; 121:e2320590121. [PMID: 38621118 DOI: 10.1073/pnas.2320590121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/06/2024] [Indexed: 04/17/2024] Open
Abstract
Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause loss of genetic diversity, populations in some environments, like Australia's arid zone, are repeatedly subject to major population fluctuations yet persist and appear able to maintain genetic diversity. Here, we use repeated population sampling over 13 y and genotype-by-sequencing of 1903 individuals to investigate the genetic consequences of repeated population fluctuations in two small mammals in the Australian arid zone. The sandy inland mouse (Pseudomys hermannsburgensis) experiences marked boom-bust population dynamics in response to the highly variable desert environment. We show that heterozygosity levels declined, and population differentiation (FST) increased, during bust periods when populations became small and isolated, but that heterozygosity was rapidly restored during episodic population booms. In contrast, the lesser hairy-footed dunnart (Sminthopsis youngsoni), a desert marsupial that maintains relatively stable population sizes, showed no linear declines in heterozygosity. These results reveal two contrasting ways in which genetic diversity is maintained in highly variable environments. In one species, diversity is conserved through the maintenance of stable population sizes across time. In the other species, diversity is conserved through rapid genetic mixing during population booms that restores heterozygosity lost during population busts.
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Affiliation(s)
- Emily J Stringer
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra ACT 2617, Australia
| | - Bernd Gruber
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra ACT 2617, Australia
| | - Stephen D Sarre
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra ACT 2617, Australia
| | - Glenda M Wardle
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Christopher R Dickman
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Aaron C Greenville
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Richard P Duncan
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra ACT 2617, Australia
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25
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Hu M, Kim I, Morán I, Peng W, Sun O, Bonnefond A, Khamis A, Bonàs-Guarch S, Froguel P, Rutter GA. Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function. FASEB J 2024; 38:e23610. [PMID: 38661000 DOI: 10.1096/fj.202301700rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
Variants at the SLC30A8 locus are associated with type 2 diabetes (T2D) risk. The lead variant, rs13266634, encodes an amino acid change, Arg325Trp (R325W), at the C-terminus of the secretory granule-enriched zinc transporter, ZnT8. Although this protein-coding variant was previously thought to be the sole driver of T2D risk at this locus, recent studies have provided evidence for lowered expression of SLC30A8 mRNA in protective allele carriers. In the present study, we examined multiple variants that influence SLC30A8 allele-specific expression. Epigenomic mapping has previously identified an islet-selective enhancer cluster at the SLC30A8 locus, hosting multiple T2D risk and cASE associations, which is spatially associated with the SLC30A8 promoter and additional neighboring genes. Here, we show that deletion of variant-bearing enhancer regions using CRISPR-Cas9 in human-derived EndoC-βH3 cells lowers the expression of SLC30A8 and several neighboring genes and improves glucose-stimulated insulin secretion. While downregulation of SLC30A8 had no effect on beta cell survival, loss of UTP23, RAD21, or MED30 markedly reduced cell viability. Although eQTL or cASE analyses in human islets did not support the association between these additional genes and diabetes risk, the transcriptional regulator JQ1 lowered the expression of multiple genes at the SLC30A8 locus and enhanced stimulated insulin secretion.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Innah Kim
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Ignasi Morán
- Life Sciences Department, Barcelona Supercomputing Center (BSC-CNS), Barcelona, Spain
| | - Weicong Peng
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Orien Sun
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Amélie Bonnefond
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
- Inserm U1283, CNRS UMR 8199, EGID, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
| | - Amna Khamis
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
- Inserm U1283, CNRS UMR 8199, EGID, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
| | - Sílvia Bonàs-Guarch
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
- Center for Genomic Regulation (CRG), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain
| | - Philippe Froguel
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
- Inserm U1283, CNRS UMR 8199, EGID, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, Québec, Canada
- Lee Kong Chian Imperial Medical School, Nanyang Technological University, Singapore, Singapore
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26
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He K, Liang C, Ma S, Liu H, Zhu Y. Copy number and selection of MHC genes in ruminants are related to habitat, average life span and diet. Gene 2024; 904:148179. [PMID: 38242373 DOI: 10.1016/j.gene.2024.148179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The ruminants, as the main group of livestock, have been extensively studied in terms of their physiology, endocrinology, biochemistry, genetics, and nutrition. Despite the wide geographic distribution and habitat diversity of animals in this group, their ecology and evolution remain poorly understood. In this study, we analyzed the gene copy number, selection, and ecological and evolutionary processes that have affected the evolution of major histocompatibility complex (MHC) genes across ruminant lineages based on available genomic data. The 51 species analyzed represented all six families of ruminants. Our finding indicated that the architecture of the MHC region is conserved in ruminants, but with variable copy numbers of MHC-I, MHC-IIA, and MHC-IIB genes. No lineage-specific gene duplication was observed in the MHC genes. The phylogenetic generalized least squares regression (PGLS) model revealed association between ecological and biological factors (habitat and lifespan) and gene duplication in DQA and DQB, but not in DRB. The selection pressure of DQA and DQB were related with lifespan, diet, and the ratio of genetic repeat elements. These results suggest that the MHC evolution in ruminants, including copy number and selection, has been influenced by genetic repeat elements, pathogen exposure risk, and intrinsic cost of possessing multiple MHC genes.
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Affiliation(s)
- Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Chunhong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Shujuan Ma
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China.
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Chai W, Yang B, Zhao S, Guo Z, Zhu L, Fan J, Yang W, Zhao W, Hao Y, Lü J, Sun W, Zhang C. [Characterization of sequences, expression profiling, and natural allelic variation analysis of the MYC gene family in sorghum ( Sorghum bicolor)]. Sheng Wu Gong Cheng Xue Bao 2024; 40:1170-1194. [PMID: 38658156 DOI: 10.13345/j.cjb.230641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Sorghum aphid (Melanaphis sacchari) and head smut fungi (Sporisorium reilianum) infesting sorghum cause delayed growth and development, and reduce yield and quality. This study use bioinformatics and molecular biological approaches to profile the gene expression pattern during sorghum development and under pest infestation, and analyzed the natural allelic DNA variation of sorghum MYC gene family. The findings provide insights for potential application in breeding the stress resistant and high productivity sorghum varieties. The results indicated that there are 28 MYC genes identified in sorghum genome, distributed on 10 chromosomes. The bHLH_MYC_N and HLH domains are the conserved domains of the MYC gene in sorghum. Gene expression analysis showed that SbbHLH35.7g exhibited high expression levels in leaves, SbAbaIn showed strong expression in early grains, and SbMYC2.1g showed high expression levels in mature pollen. In anti-aphid strains at the 5-leaf stage, SbAbaIn, SbLHW.4g and SbLHW.2g were significantly induced in leaves, while SbbHLH35.7g displayed the highest expression level in panicle tissue, which was significantly induced by the infection of head smut. Promoter cis-element analysis identified methyl jasmonate (MJ), abscisic acid (ABA), salicylic acid (SA) and MYB-binding sites related to drought-stress inducibility. Furthermore, genomic resequencing data analysis revealed natural allelic DNA variations such as single nucleotide polymorphism (SNP) and insertion-deletion (INDEL) for the key SbMYCs. Protein interaction network analysis using STRING indicated that SbAbaIn interacts with TIFYdomain protein, and SbbHLH35.7g interacts with MDR and imporin. SbMYCs exhibited temporal and spatial expression patterns and played vital roles during the sorghum development. Infestation by sugarcane aphids and head smut fungi induced the expression of SbAbaIn and SbbHLH35.7g, respectively. SbAbaIn modulated the jasmonic acid (JA) pathway to regulate the expression of defensive genes, conferring resistance to insects. On the other hand, SbbHLH35.7g participated in detoxification reactions to defend against pathogens.
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Affiliation(s)
- Wenting Chai
- Functional Grains Innovation Center of State Grain Administration, Loess Plateau Crop Collaborative Innovation Center jointly built by Ministry of Education, College of Forestry, College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Bohui Yang
- Functional Grains Innovation Center of State Grain Administration, Loess Plateau Crop Collaborative Innovation Center jointly built by Ministry of Education, College of Forestry, College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Shanshan Zhao
- Functional Grains Innovation Center of State Grain Administration, Loess Plateau Crop Collaborative Innovation Center jointly built by Ministry of Education, College of Forestry, College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Zhiqiang Guo
- Functional Grains Innovation Center of State Grain Administration, Loess Plateau Crop Collaborative Innovation Center jointly built by Ministry of Education, College of Forestry, College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Lixun Zhu
- Functional Grains Innovation Center of State Grain Administration, Loess Plateau Crop Collaborative Innovation Center jointly built by Ministry of Education, College of Forestry, College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Jiali Fan
- Functional Grains Innovation Center of State Grain Administration, Loess Plateau Crop Collaborative Innovation Center jointly built by Ministry of Education, College of Forestry, College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Wei Yang
- Institute for Sorghum Research, Shanxi Agricultural University, Yuci 030600, Shanxi, China
| | - Weijun Zhao
- Institute for Sorghum Research, Shanxi Agricultural University, Yuci 030600, Shanxi, China
| | - Yanping Hao
- Functional Grains Innovation Center of State Grain Administration, Loess Plateau Crop Collaborative Innovation Center jointly built by Ministry of Education, College of Forestry, College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Jinhui Lü
- Functional Grains Innovation Center of State Grain Administration, Loess Plateau Crop Collaborative Innovation Center jointly built by Ministry of Education, College of Forestry, College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Wenxian Sun
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chunlai Zhang
- Functional Grains Innovation Center of State Grain Administration, Loess Plateau Crop Collaborative Innovation Center jointly built by Ministry of Education, College of Forestry, College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
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Han J, Wang H, Song J, Jia H, Zhang X, Li S, Xu C, Li Z, Yang W. [Genetic background of lily germplasm resources based on SSR markers]. Sheng Wu Gong Cheng Xue Bao 2024; 40:1211-1224. [PMID: 38658158 DOI: 10.13345/j.cjb.230862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
To study the genetic background of lily (Lilium spp.) germplasm resources, and accurately evaluate and select excellent germplasm for genetic improvement of lily, we analyzed the genetic background of 62 lily germplasm accessions from 11 provinces of China by using simple sequence repeat (SSR) molecular markers. The results showed that 15 out of 83 pairs of lily SSR primers were polymorphic. A total of 157 allelic loci were amplified, with the number of alleles per locus ranging from 5 to 19 and the average number of effective alleles per locus being 4.162 8. The average observed heterozygosity and expected heterozygosity were 0.228 2 and 0.694 1, respectively. The average polymorphic information content was 0.678 8. The average Nei's diversity index and Shannon's information index were 0.694 1 and 1.594 9, respectively, indicating that the tested lily germplasm had high genetic diversity. The 62 germplasm accessions were classified into 5 groups by the unweighted pair group method with arithmetic mean (UPGMA) and into 3 groups by the principal component analysis. The two analyses revealed a geographic correlation among different groups. The majority of lily germplasm accessions from the same source tended to cluster together. The population structure analysis classified the lily accessions into 4 populations and 1 mixed population. The above results provide a theoretical basis and genetic resources for the precise identification and breeding of lily germplasm resources.
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Affiliation(s)
- Jiaqi Han
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiping Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangping Song
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixia Jia
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaohui Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Chu Xu
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijie Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenlong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Rosa RDS, Furlan JPR, Santos LDRD, Ramos MS, Savazzi EA, Stehling EG. Genetic diversity of KPC-2-producing Klebsiella pneumoniae complex from aquatic ecosystems. World J Microbiol Biotechnol 2024; 40:177. [PMID: 38656467 DOI: 10.1007/s11274-024-03994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
During the COVID-19 pandemic, the occurrence of carbapenem-resistant Klebsiella pneumoniae increased in human clinical settings worldwide. Impacted by this increase, international high-risk clones harboring carbapenemase-encoding genes have been circulating in different sources, including the environment. The blaKPC gene is the most commonly disseminated carbapenemase-encoding gene worldwide, whose transmission is carried out by different mobile genetic elements. In this study, blaKPC-2-positive Klebsiella pneumoniae complex strains were isolated from different anthropogenically affected aquatic ecosystems and characterized using phenotypic, molecular, and genomic methods. K. pneumoniae complex strains exhibited multidrug-resistant and extensively drug-resistant profiles, spotlighting the resistance to carbapenems, ceftazidime-avibactam, colistin, and tigecycline, which are recognized as last-line antimicrobial treatment options. Molecular analysis showed the presence of several antimicrobial resistance, virulence, and metal tolerance genes. In-depth analysis showed that the blaKPC-2 gene was associated with three different Tn4401 isoforms (i.e., Tn4401a, Tn4401b, and Tn4401i) and NTEKPC elements. Different plasmid replicons were detected and a conjugative IncN-pST15 plasmid harboring the blaKPC-2 gene associated with Tn4401i was highlighted. K. pneumoniae complex strains belonging to international high-risk (e.g., ST11 and ST340) and unusual clones (e.g., ST323, ST526, and ST4216) previously linked to clinical settings. In this context, some clones were reported for the first time in the environmental sector. Therefore, these findings evidence the occurrence of carbapenemase-producing K. pneumoniae complex strains in aquatic ecosystems and contribute to the monitoring of carbapenem resistance worldwide.
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Affiliation(s)
- Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | | | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil.
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Liu M, Zhang F, Lu H, Xue H, Dong X, Li Z, Xu J, Wang W, Wei C. PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome. BMC Genomics 2024; 25:405. [PMID: 38658835 DOI: 10.1186/s12864-024-10302-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation for many individuals together with a graph-based pangenome is getting higher and higher. Here we report a new pangenome browser PPanG, a precise pangenome browser enabling nucleotide-level comparison of individual genome annotations together with a graph-based pangenome. Nine rice genomes with annotations were provided by default as potential references, and any individual genome can be selected as the reference. Our pangenome browser provides unprecedented insights on genome variations at different levels from base to gene, and reveals how the structures of a gene could differ for individuals. PPanG can be applied to any species with multiple individual genomes available and it is available at https://cgm.sjtu.edu.cn/PPanG .
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Affiliation(s)
- Mingwei Liu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Fan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Huimin Lu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hongzhang Xue
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiaorui Dong
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhikang Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jianlong Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Wensheng Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
| | - Chaochun Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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31
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Inotani T, Horaguchi A, Morishita Y, Yoshida A, Otomo M, Suzuki M, Inui T, Okubo Y, Komatsu S, Mizuno C, Takahashi Y, Ochiai T, Kinjo T, Asato T, Takayama J, Tamiya G, Saijo N, Kikuchi A, Haginoya K. Treatment of ZC4H2 Variant-Associated Spastic Paraplegia with Selective Dorsal Rhizotomy and Intensive Postoperative Rehabilitation: A Case Report. TOHOKU J EXP MED 2024; 262:239-244. [PMID: 38267061 DOI: 10.1620/tjem.2024.j004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Selective dorsal rhizotomy (SDR) has been used to treat children with spastic cerebral palsy (CP), and its beneficial effect on quality of life and ambulation has been confirmed in long-term follow-up studies. However, the role of SDR in the treatment of spasticity in patients with hereditary spastic paraplegia (HSP) and related disorders is not well-established. Here, we report the first patient with the ZC4H2 variant who underwent SDR to treat spastic paraplegia. Abnormal gait was discovered during a regular checkup at the age of 3 years and 9 months, and she was diagnosed with spastic paraplegia. She was heterozygous for the ZC4H2 variant and underwent SDR at the age of 5 years and 11 months, which alleviated the spasticity. The patient underwent inpatient postoperative rehabilitation for 4 months and continued outpatient physiotherapy after discharge. The Gross Motor Function Measure-88 score and maximum walking speed decreased transiently 1 month postoperatively, but gradually recovered, and continuously improved 6 months postoperatively. SDR and postoperative intensive rehabilitation were effective in improving motor and walking functions up to 6 months after surgery, although long-term follow-up is needed to draw conclusions.
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Affiliation(s)
- Toshiki Inotani
- Department of Rehabilitation and Developmental Support, Miyagi Children's Hospital
| | - Akira Horaguchi
- Department of Rehabilitation and Developmental Support, Miyagi Children's Hospital
| | - Yuko Morishita
- Department of Rehabilitation and Developmental Support, Miyagi Children's Hospital
| | - Ayuko Yoshida
- Department of Rehabilitation and Developmental Support, Miyagi Children's Hospital
| | - Misaki Otomo
- Department of Rehabilitation and Developmental Support, Miyagi Children's Hospital
| | - Makoto Suzuki
- Graduate School of Health and Environment Sciences, Tohoku Bunka Gakuen University
| | - Takehiko Inui
- Department of Pediatric Neurology, Miyagi Children's Hospital
| | - Yukimune Okubo
- Department of Pediatric Neurology, Miyagi Children's Hospital
| | - Shigemasa Komatsu
- Department of Pediatric Orthopedic Surgery and Rehabilitation, Miyagi Children's Hospital
| | - Chika Mizuno
- Department of Pediatric Orthopedic Surgery and Rehabilitation, Miyagi Children's Hospital
| | - Yuko Takahashi
- Department of Pediatric Orthopedic Surgery and Rehabilitation, Miyagi Children's Hospital
| | - Tatsuhiro Ochiai
- Department of Pediatric Orthopedic Surgery and Rehabilitation, Miyagi Children's Hospital
| | - Takeshi Kinjo
- Department of Orthopedic Surgery and Rehabilitation, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center
| | - Takashi Asato
- Department of Orthopedic Surgery and Rehabilitation, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center
| | - Jun Takayama
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine
- Tohoku Medical Megabank Organization, Tohoku University
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine
| | - Gen Tamiya
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine
- Tohoku Medical Megabank Organization, Tohoku University
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine
| | - Naoya Saijo
- Department of Pediatrics, Tohoku University School of Medicine
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University School of Medicine
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine
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32
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Guyon L, Guez J, Toupance B, Heyer E, Chaix R. Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck. Nat Commun 2024; 15:3243. [PMID: 38658560 DOI: 10.1038/s41467-024-47618-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
Studies have found a pronounced decline in male effective population sizes worldwide around 3000-5000 years ago. This bottleneck was not observed for female effective population sizes, which continued to increase over time. Until now, this remarkable genetic pattern was interpreted as the result of an ancient structuring of human populations into patrilineal groups (gathering closely related males) violently competing with each other. In this scenario, violence is responsible for the repeated extinctions of patrilineal groups, leading to a significant reduction in male effective population size. Here, we propose an alternative hypothesis by modelling a segmentary patrilineal system based on anthropological literature. We show that variance in reproductive success between patrilineal groups, combined with lineal fission (i.e., the splitting of a group into two new groups of patrilineally related individuals), can lead to a substantial reduction in the male effective population size without resorting to the violence hypothesis. Thus, a peaceful explanation involving ancient changes in social structures, linked to global changes in subsistence systems, may be sufficient to explain the reported decline in Y-chromosome diversity.
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Affiliation(s)
- Léa Guyon
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France.
| | - Jérémy Guez
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France
- Université Paris-Saclay, CNRS, INRIA, Laboratoire Interdisciplinaire des Sciences du Numérique, Orsay, 91400, France
| | - Bruno Toupance
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France
- Université Paris Cité, Eco-anthropologie, Paris, F-75006, France
| | - Evelyne Heyer
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France
| | - Raphaëlle Chaix
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France.
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Buthasane W, Shotelersuk V, Chetruengchai W, Srichomthong C, Assawapitaksakul A, Tangphatsornruang S, Pootakham W, Sonthirod C, Tongsima S, Wangkumhang P, Wilantho A, Thongphakdee A, Sanannu S, Poksawat C, Nipanunt T, Kasorndorkbua C, Koepfli KP, Pukazhenthi BS, Suriyaphol P, Wongsurawat T, Jenjaroenpun P, Suriyaphol G. Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures. Sci Rep 2024; 14:9455. [PMID: 38658744 DOI: 10.1038/s41598-024-59990-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The Asian king vulture (AKV), a vital forest scavenger, is facing globally critical endangerment. This study aimed to construct a reference genome to unveil the mechanisms underlying its scavenger abilities and to assess the genetic relatedness of the captive population in Thailand. A reference genome of a female AKV was assembled from sequencing reads obtained from both PacBio long-read and MGI short-read sequencing platforms. Comparative genomics with New World vultures (NWVs) and other birds in the Family Accipitridae revealed unique gene families in AKV associated with retroviral genome integration and feather keratin, contrasting with NWVs' genes related to olfactory reception. Expanded gene families in AKV were linked to inflammatory response, iron regulation and spermatogenesis. Positively selected genes included those associated with anti-apoptosis, immune response and muscle cell development, shedding light on adaptations for carcass consumption and high-altitude soaring. Using restriction site-associated DNA sequencing (RADseq)-based genome-wide single nucleotide polymorphisms (SNPs), genetic relatedness and inbreeding status of five captive AKVs were determined, revealing high genomic inbreeding in two females. In conclusion, the AKV reference genome was established, providing insights into its unique characteristics. Additionally, the potential of RADseq-based genome-wide SNPs for selecting AKV breeders was demonstrated.
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Affiliation(s)
- Wannapol Buthasane
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Alisa Wilantho
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Ampika Thongphakdee
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Saowaphang Sanannu
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Chaianan Poksawat
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Tarasak Nipanunt
- Huai Kha Khaeng Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Uthai Thani, 61160, Thailand
| | - Chaiyan Kasorndorkbua
- Laboratory of Raptor Research and Conservation Medicine, Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, 22630, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Prapat Suriyaphol
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Xu J, Wang Y, Wu K, Chen J. Identification and characterization of functionally relevant SSR markers in natural Dalbergia odorifera populations. BMC Plant Biol 2024; 24:315. [PMID: 38654191 DOI: 10.1186/s12870-024-05019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Dalbergia odorifera is a rare and precious rosewood specie, which is valued for its amber tones, abstract figural patterns, and impermeability to water and insects. However, the information on genetic diversity and marker-assisted selection breeding of D. odorifera is still limited. Simple sequence repeat (SSR) markers are an ideal tool for genetic diversity analysis and marker-assisted molecular breeding for complex traits. RESULTS Here, we have developed SSR markers within candidate genes and used them to explore the genetic diversity among D. odorifera germplasm resources. A total of 635 SSR loci were identified. The proportions of mono-, di- and tri-nucleotide repeat motifs were 52.28%, 22.99% and 21.42%, respectively. From these, a total of 114 SSR primers were synthesized, of which 24 SSR markers displayed polymorphism (polymorphic information content (PIC) > 0.25). Subsequently, these polymorphic markers were used for the genetic diversity analysis of 106 D. odorifera individuals from 11 natural populations. According to the genetic diversity analysis of D. odorifera natural populations, the average observed heterozygosity (Ho) was 0.500, the average expected heterozygosity (He) was 0.524, and the average Shannon's information index (I) was 0.946. These indicated that the natural populations had moderate genetic diversity. AMOVA analysis showed that 5% of the total variation was within the individuals of a population, whereas 95% of the variation was among the individuals of the populations, indicating a high degree of genetic variation between populations. On the basis of their genetic structures, these populations could be divided into four groups. CONCLUSIONS Our study provides important experimental resources for genetic studies and assists in the program of molecular breeding of D. odorifera wood formation.
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Affiliation(s)
- Jieru Xu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yue Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Kunlin Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Jinhui Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, China.
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China.
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Yu XQ. [Current status and prospects of genetic research on IgA nephropathy]. Zhonghua Yi Xue Za Zhi 2024; 104:1351-1355. [PMID: 38644282 DOI: 10.3760/cma.j.cn112137-20231122-01155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
IgA nephropathy is the most common primary glomerulonephritis worldwide, and genetic factors may play an important role in its pathogenesis. Following candidate gene association analysis and genome-wide linkage study, genome-wide association studies (GWAS) have found multiple susceptibility genes related to the pathogenesis and clinical phenotype of IgA nephropathy. Meanwhile, structural variation and epigenetic changes are also closely related to IgA nephropathy. Genetic variants have been found to explain about 11% of its heritability. In the current era of genomic medicine, how to find more susceptible genes/loci, whole genome sequencing studies (WGS) provide clues to further understand the genetic variation of IgA nephropathy. How to find the cell type-specific susceptibility genes associated with IgA nephropathy, multi-omics studies will conduct comprehensive analysis via single-cell sequencing, expression quantitative trait locus (eQTL) and genomics to find the pathogenic genes and offer insights into the development of targeted drugs, which will be the trend and direction of future research.
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Affiliation(s)
- X Q Yu
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
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Gu X, Li L, Zhong X, Su Y, Wang T. The size diversity of the Pteridaceae family chloroplast genome is caused by overlong intergenic spacers. BMC Genomics 2024; 25:396. [PMID: 38649816 PMCID: PMC11036588 DOI: 10.1186/s12864-024-10296-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND While the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to play a pivotal role in determining the size of Pteridaceae cpDNAs. This provides an opportunity to delve into the evolution of chloroplast genomic structures of the Pteridaceae family. This study added five Pteridaceae species, comparing them with 36 published counterparts. RESULTS Poor alignment in the non-coding regions of the Pteridaceae family was observed, and this was attributed to the widespread presence of overlong IGSs in Pteridaceae cpDNAs. These overlong IGSs were identified as a major factor influencing variations in cpDNA size. In comparison to non-expanded IGSs, overlong IGSs exhibited significantly higher GC content and were rich in repetitive sequences. Species divergence time estimations suggest that these overlong IGSs may have already existed during the early radiation of the Pteridaceae family. CONCLUSIONS This study reveals new insights into the genetic variation, evolutionary history, and dynamic changes in the cpDNA structure of the Pteridaceae family, providing a fundamental resource for further exploring its evolutionary research.
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Affiliation(s)
- Xiaolin Gu
- College of Life Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Lingling Li
- College of Life Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Xiaona Zhong
- College of Life Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China.
- Research Institute of Sun Yat-sen University in Shenzhen, 518057, Shenzhen, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, 510642, Guangzhou, China.
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Li YD, Liu YC, Jiang YX, Namisy A, Chung WH, Sun YH, Chen SY. Analyzing genetic diversity in luffa and developing a Fusarium wilt-susceptible linked SNP marker through a single plant genome-wide association (sp-GWAS) study. BMC Plant Biol 2024; 24:307. [PMID: 38644483 PMCID: PMC11034075 DOI: 10.1186/s12870-024-05022-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 04/15/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Luffa (Luffa spp.) is an economically important crop of the Cucurbitaceae family, commonly known as sponge gourd or vegetable gourd. It is an annual cross-pollinated crop primarily found in the subtropical and tropical regions of Asia, Australia, Africa, and the Americas. Luffa serves not only as a vegetable but also exhibits medicinal properties, including anti-inflammatory, antidiabetic, and anticancer effects. Moreover, the fiber derived from luffa finds extensive applications in various fields such as biotechnology and construction. However, luffa Fusarium wilt poses a severe threat to its production, and existing control methods have proven ineffective in terms of cost-effectiveness and environmental considerations. Therefore, there is an urgent need to develop luffa varieties resistant to Fusarium wilt. Single-plant GWAS (sp-GWAS) has been demonstrated as a promising tool for the rapid and efficient identification of quantitative trait loci (QTLs) associated with target traits, as well as closely linked molecular markers. RESULTS In this study, a collection of 97 individuals from 73 luffa accessions including two major luffa species underwent single-plant GWAS to investigate luffa Fusarium wilt resistance. Utilizing the double digest restriction site associated DNA (ddRAD) method, a total of 8,919 high-quality single nucleotide polymorphisms (SNPs) were identified. The analysis revealed the potential for Fusarium wilt resistance in accessions from both luffa species. There are 6 QTLs identified from 3 traits, including the area under the disease progress curve (AUDPC), a putative disease-resistant QTL, was identified on the second chromosome of luffa. Within the region of linkage disequilibrium, a candidate gene homologous to LOC111009722, which encodes peroxidase 40 and is associated with disease resistance in Cucumis melo, was identified. Furthermore, to validate the applicability of the marker associated with resistance from sp-GWAS, an additional set of 21 individual luffa plants were tested, exhibiting 93.75% accuracy in detecting susceptible of luffa species L. aegyptiaca Mill. CONCLUSION In summary, these findings give a hint of genome position that may contribute to luffa wild resistance to Fusarium and can be utilized in the future luffa wilt resistant breeding programs aimed at developing wilt-resistant varieties by using the susceptible-linked SNP marker.
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Affiliation(s)
- Yun-Da Li
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
| | - Yu-Chi Liu
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
| | - Yu-Xuan Jiang
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
| | - Ahmed Namisy
- Department of Plant Pathology, National Chung-Hsing University, Taichung, Taiwan
| | - Wen-Hsin Chung
- Department of Plant Pathology, National Chung-Hsing University, Taichung, Taiwan
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung-Hsing University, Taichung, Taiwan
| | - Shu-Yun Chen
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan.
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Gaston JM, Alm EJ, Zhang AN. Fast and accurate variant identification tool for sequencing-based studies. BMC Biol 2024; 22:90. [PMID: 38644496 PMCID: PMC11034086 DOI: 10.1186/s12915-024-01891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/17/2024] [Indexed: 04/23/2024] Open
Abstract
BACKGROUND Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, and disease diagnosis. Genetic studies into microbiomes often require processing numerous sequencing datasets, necessitating variant identifiers with high speed, accuracy, and robustness. RESULTS We present QuickVariants, a bioinformatics tool that effectively summarizes variant information from read alignments and identifies variants. When tested on diverse bacterial sequencing data, QuickVariants demonstrates a ninefold higher median speed than bcftools, a widely used variant identifier, with higher accuracy in identifying both point mutations and indels. This accuracy extends to variant identification in virus samples, including SARS-CoV-2, particularly with significantly fewer false negative indels than bcftools. The high accuracy of QuickVariants is further demonstrated by its detection of a greater number of Omicron-specific indels (5 versus 0) and point mutations (61 versus 48-54) than bcftools in sewage metagenomes predominated by Omicron variants. Much of the reduced accuracy of bcftools was attributable to its misinterpretation of indels, often producing false negative indels and false positive point mutations at the same locations. CONCLUSIONS We introduce QuickVariants, a fast, accurate, and robust bioinformatics tool designed for identifying genetic variants for microbial studies. QuickVariants is available at https://github.com/caozhichongchong/QuickVariants .
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Affiliation(s)
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, USA
| | - An-Ni Zhang
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, USA.
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Innella G, Ferrari S, Miccoli S, Luppi E, Fortuno C, Parsons MT, Spurdle AB, Turchetti D. Clinical implications of VUS reclassification in a single-centre series from application of ACMG/AMP classification rules specified for BRCA1/2. J Med Genet 2024; 61:483-489. [PMID: 38160042 DOI: 10.1136/jmg-2023-109694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND BRCA1/2 testing is crucial to guide clinical decisions in patients with hereditary breast/ovarian cancer, but detection of variants of uncertain significance (VUSs) prevents proper management of carriers. The ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) BRCA1/2 Variant Curation Expert Panel (VCEP) has recently developed BRCA1/2 variant classification guidelines consistent with ClinGen processes, specified against the ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular-Pathology) classification framework. METHODS The ClinGen-approved BRCA1/2-specified ACMG/AMP classification guidelines were applied to BRCA1/2 VUSs identified from 2011 to 2022 in a series of patients, retrieving information from the VCEP documentation, public databases, literature and ENIGMA unpublished data. Then, we critically re-evaluated carrier families based on new results and checked consistency of updated classification with main sources for clinical interpretation of BRCA1/2 variants. RESULTS Among 166 VUSs detected in 231 index cases, 135 (81.3%) found in 197 index cases were classified by applying BRCA1/2-specified ACMG/AMP criteria: 128 (94.8%) as Benign/Likely Benign and 7 (5.2%) as Pathogenic/Likely Pathogenic. The average time from the first report as 'VUS' to classification using this approach was 49.4 months. Considering that 15 of these variants found in 64 families had already been internally reclassified prior to this work, this study provided 121 new reclassifications among the 151 (80.1%) remaining VUSs, relevant to 133/167 (79.6%) families. CONCLUSIONS These results demonstrated the effectiveness of new BRCA1/2 ACMG/AMP classification guidelines for VUS classification within a clinical cohort, and their important clinical impact. Furthermore, they suggested a cadence of no more than 3 years for regular review of VUSs, which however requires time, expertise and resources.
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Affiliation(s)
- Giovanni Innella
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Simona Ferrari
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Sara Miccoli
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Elena Luppi
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Michael T Parsons
- Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Daniela Turchetti
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Peruchet-Noray L, Sedlmeier AM, Dimou N, Baurecht H, Fervers B, Fontvieille E, Konzok J, Tsilidis KK, Christakoudi S, Jansana A, Cordova R, Bohmann P, Stein MJ, Weber A, Bézieau S, Brenner H, Chan AT, Cheng I, Figueiredo JC, Garcia-Etxebarria K, Moreno V, Newton CC, Schmit SL, Song M, Ulrich CM, Ferrari P, Viallon V, Carreras-Torres R, Gunter MJ, Freisling H. Tissue-specific genetic variation suggests distinct molecular pathways between body shape phenotypes and colorectal cancer. Sci Adv 2024; 10:eadj1987. [PMID: 38640244 PMCID: PMC11029802 DOI: 10.1126/sciadv.adj1987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/12/2024] [Indexed: 04/21/2024]
Abstract
It remains unknown whether adiposity subtypes are differentially associated with colorectal cancer (CRC). To move beyond single-trait anthropometric indicators, we derived four multi-trait body shape phenotypes reflecting adiposity subtypes from principal components analysis on body mass index, height, weight, waist-to-hip ratio, and waist and hip circumference. A generally obese (PC1) and a tall, centrally obese (PC3) body shape were both positively associated with CRC risk in observational analyses in 329,828 UK Biobank participants (3728 cases). In genome-wide association studies in 460,198 UK Biobank participants, we identified 3414 genetic variants across four body shapes and Mendelian randomization analyses confirmed positive associations of PC1 and PC3 with CRC risk (52,775 cases/45,940 controls from GECCO/CORECT/CCFR). Brain tissue-specific genetic instruments, mapped to PC1 through enrichment analysis, were responsible for the relationship between PC1 and CRC, while the relationship between PC3 and CRC was predominantly driven by adipose tissue-specific genetic instruments. This study suggests distinct putative causal pathways between adiposity subtypes and CRC.
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Affiliation(s)
- Laia Peruchet-Noray
- International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, 69366 Lyon CEDEX 07, France
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Anja M. Sedlmeier
- Center for Translational Oncology, University Hospital Regensburg, Regensburg, Germany
- Bavarian Cancer Research Center (BZKF), Regensburg, Germany
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Niki Dimou
- International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, 69366 Lyon CEDEX 07, France
| | - Hansjörg Baurecht
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Béatrice Fervers
- Département Prévention Cancer Environnement, Centre Léon Bérard, Lyon, France
| | - Emma Fontvieille
- International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, 69366 Lyon CEDEX 07, France
| | - Julian Konzok
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Kostas K. Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary’s Campus, Norfolk Place, London W2 1PG, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Sofia Christakoudi
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary’s Campus, Norfolk Place, London W2 1PG, UK
- Department of Inflammation Biology, School of Immunology & Microbial Sciences, King’s College London, London, UK
| | - Anna Jansana
- International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, 69366 Lyon CEDEX 07, France
| | - Reynalda Cordova
- International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, 69366 Lyon CEDEX 07, France
- Department of Nutritional Sciences, University of Vienna, Vienna, Austria
| | - Patricia Bohmann
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Michael J. Stein
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Andrea Weber
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jane C. Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Koldo Garcia-Etxebarria
- Biodonostia, Gastrointestinal Genetics Group, San Sebastián, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Victor Moreno
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | | | - Stephanie L. Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Departments of Epidemiology and Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cornelia M. Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Pietro Ferrari
- International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, 69366 Lyon CEDEX 07, France
| | - Vivian Viallon
- International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, 69366 Lyon CEDEX 07, France
| | - Robert Carreras-Torres
- Digestive Diseases and Microbiota Group, Girona Biomedical Research Institute (IDIBGI), Salt, Girona, Spain
| | - Marc J. Gunter
- International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, 69366 Lyon CEDEX 07, France
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary’s Campus, Norfolk Place, London W2 1PG, UK
| | - Heinz Freisling
- International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, 69366 Lyon CEDEX 07, France
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Costa JND, Siqueira JAM, Teixeira DM, Lobo PDS, Guerra SDFDS, Souza IM, Cardoso BTM, Farias LSS, Resque HR, Gabbay YB, Silva LDD. Epidemiological and molecular surveillance of norovirus in the Brazilian Amazon: description of recombinant genotypes and improvement of evolutionary analysis. Rev Inst Med Trop Sao Paulo 2024; 66:e22. [PMID: 38656038 DOI: 10.1590/s1678-9946202466022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/12/2024] [Indexed: 04/26/2024] Open
Abstract
Noroviruses are highly infectious, genetically diverse viruses. Global outbreaks occur frequently, making molecular surveillance important for infection monitoring. This cross-sectional descriptive study aimed to monitor cases of norovirus gastroenteritis in the Brazilian Amazon. Fecal samples were tested by immunoenzymatic assay, RT-PCR and genetic sequencing for the ORF1/ORF2 and protease regions. Bayesian inference with a molecular clock was employed to construct the phylogeny. The norovirus prevalence was 25.8%, with a higher positivity rate among children aged 0-24 months. Genogroup GII accounted for 98.1% of the sequenced samples, while GI accounted for 1.9% of them. The GII.P16/GII.4 genotype was the most prevalent, with an evolution rate of 2.87x10-3 and TMRCA estimated in 2012. This study demonstrates that norovirus is a primary causative agent of gastroenteritis and provides data on viral genetic diversity that may facilitate infection surveillance and vaccine development.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hugo Reis Resque
- Instituto Evandro Chagas, Seção de Virologia, Ananindeua, Pará, Brazil
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Chen J, Liu C, Li W, Zhang W, Wang Y, Clark AG, Lu J. From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics. Sci Adv 2024; 10:eadh3425. [PMID: 38630810 PMCID: PMC11023512 DOI: 10.1126/sciadv.adh3425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.
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Affiliation(s)
- Junhao Chen
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Liu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weixuan Li
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenxia Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yirong Wang
- College of Biology, Hunan University, Changsha 410082, China
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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García-Castro KL, Márquez EJ. Temporal analysis of genetic diversity and gene flow in the threatened catfish Pseudoplatystoma magdaleniatum from a dammed neotropical river. PLoS One 2024; 19:e0301577. [PMID: 38635781 PMCID: PMC11025948 DOI: 10.1371/journal.pone.0301577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
The striped catfish Pseudoplatystoma magdaleniatum is a large-sized migratory species from the north Andes region, endemic to Magdalena basin and one of the major fishery resources. Despite the estimated reduction of over 80% of the fisheries production of this species throughout the basin in recent decades, its population in the lower Magdalena-Cauca basin showed healthy genetics after molecular analyses. However, the current conservation status of this species and several habitat disturbances demand the re-evaluation of its population genetics to infer evolutionary risks and assess potential changes. This work analyzed a total of 164 samples from the Cauca River collected downstream the Ituango Dam between 2019-2021 using species-specific microsatellite markers to compare the genetic diversity and structure in samples collected between 2010-2014 from the lower Magdalena-Cauca basin, previously analyzed. Our results showed a relatively stable panmictic population over time (4 to 10 years), with high genetic diversity and evidence of recent bottleneck. Promoting habitat connectivity to conserve gene flow, characterizing diversity and genetic structure over the entire basin, and integrating the results with future monitoring are important aspects for the management planning for P. magdaleniatum in the Magdalena-Cauca basin.
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Affiliation(s)
- Kevin León García-Castro
- Facultad de Ciencias Universidad Nacional de Colombia–Sede Medellín, Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Medellín, Antioquia, Colombia
| | - Edna Judith Márquez
- Facultad de Ciencias Universidad Nacional de Colombia–Sede Medellín, Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Medellín, Antioquia, Colombia
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Zhao P, Wang C, Sun S, Wang X, Balch WE. Tracing genetic diversity captures the molecular basis of misfolding disease. Nat Commun 2024; 15:3333. [PMID: 38637533 PMCID: PMC11026414 DOI: 10.1038/s41467-024-47520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Genetic variation in human populations can result in the misfolding and aggregation of proteins, giving rise to systemic and neurodegenerative diseases that require management by proteostasis. Here, we define the role of GRP94, the endoplasmic reticulum Hsp90 chaperone paralog, in managing alpha-1-antitrypsin deficiency on a residue-by-residue basis using Gaussian process regression-based machine learning to profile the spatial covariance relationships that dictate protein folding arising from sequence variants in the population. Covariance analysis suggests a role for the ATPase activity of GRP94 in controlling the N- to C-terminal cooperative folding of alpha-1-antitrypsin responsible for the correction of liver aggregation and lung-disease phenotypes of alpha-1-antitrypsin deficiency. Gaussian process-based spatial covariance profiling provides a standard model built on covariant principles to evaluate the role of proteostasis components in guiding information flow from genome to proteome in response to genetic variation, potentially allowing us to intervene in the onset and progression of complex multi-system human diseases.
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Affiliation(s)
- Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- Department of Nutrition and Food Hygiene, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Collaborative Innovation Center for Cancer Personalized Medicine, and Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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He S, Xu B, Chen S, Li G, Zhang J, Xu J, Wu H, Li X, Yang Z. Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome. BMC Genomics 2024; 25:384. [PMID: 38637729 PMCID: PMC11027378 DOI: 10.1186/s12864-024-10278-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear. RESULTS We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species. CONCLUSIONS These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.
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Affiliation(s)
- Shuilian He
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Bin Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Siyun Chen
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Gengyun Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Jie Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Junqiang Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Hang Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Xuejiao Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
| | - Zhengan Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
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Adu GB, Awuku FJ, Garcia-Oliveira AL, Amegbor IK, Nelimor C, Nboyine J, Karikari B, Atosona B, Manigben KA, Aboyadana PA. DArTseq-based SNP markers reveal high genetic diversity among early generation fall armyworm tolerant maize inbred lines. PLoS One 2024; 19:e0294863. [PMID: 38630672 PMCID: PMC11023204 DOI: 10.1371/journal.pone.0294863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/09/2023] [Indexed: 04/19/2024] Open
Abstract
Diversity analysis using molecular markers serves as a powerful tool in unravelling the intricacies of inclusivity within various populations and is an initial step in the assessment of populations and the development of inbred lines for host plant resistance in maize. This study was conducted to assess the genetic diversity and population structure of 242 newly developed S3 inbred lines using 3,305 single nucleotide polymorphism (SNP) markers and to also assess the level of homozygosity achieved in each of the inbred lines. A total of 1,184 SNP markers were found highly informative, with a mean polymorphic information content (PIC) of 0.23. Gene diversity was high among the inbred lines, ranging from 0.04 to 0.50, with an average of 0.27. The residual heterozygosity of the 242 S3 inbred lines averaged 8.8%, indicating moderately low heterozygosity levels among the inbred lines. Eighty-four percent of the 58,322 pairwise kinship coefficients among the inbred lines were near zero (0.00-0.05), with only 0.3% of them above 0.50. These results revealed that many of the inbred lines were distantly related, but none were redundant, suggesting each inbred line had a unique genetic makeup with great potential to provide novel alleles for maize improvement. The admixture-based structure analysis, principal coordinate analysis, and neighbour-joining clustering were concordant in dividing the 242 inbred lines into three subgroups based on the pedigree and selection history of the inbred lines. These findings could guide the effective use of the newly developed inbred lines and their evaluation in quantitative genetics and molecular studies to identify candidate lines for breeding locally adapted fall armyworm tolerant varieties in Ghana and other countries in West and Central Africa.
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Affiliation(s)
| | | | - Ana Luisa Garcia-Oliveira
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
- Department of Molecular Biology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, Haryana, India
| | - Isaac Kodzo Amegbor
- CSIR-Savanna Agricultural Research Institute, Nyankpala, Ghana
- Faculty of Natural and Agricultural Sciences, Department of Plant Breeding, University of the Free State, Bloemfontein, South Africa
| | - Charles Nelimor
- CSIR-Savanna Agricultural Research Institute, Nyankpala, Ghana
| | - Jerry Nboyine
- CSIR-Savanna Agricultural Research Institute, Nyankpala, Ghana
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
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Sterzi L, Nodari R, Di Marco F, Ferrando ML, Saluzzo F, Spitaleri A, Allahverdi H, Papaleo S, Panelli S, Rimoldi SG, Batisti Biffignandi G, Corbella M, Cavallero A, Prati P, Farina C, Cirillo DM, Zuccotti G, Bandi C, Comandatore F. Genetic barriers more than environmental associations explain Serratia marcescens population structure. Commun Biol 2024; 7:468. [PMID: 38632370 PMCID: PMC11023947 DOI: 10.1038/s42003-024-06069-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.
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Affiliation(s)
- Lodovico Sterzi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Riccardo Nodari
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Federico Di Marco
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Laura Ferrando
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Saluzzo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Hamed Allahverdi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Stella Papaleo
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Sara Giordana Rimoldi
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, Milan, Italy
| | | | - Marta Corbella
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
| | | | - Paola Prati
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Pavia, Italy
| | - Claudio Farina
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, Bergamo, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
- Department of Paediatrics, Children's Hospital "V. Buzzi", Milano, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo Ed Enrica Invernizzi", University of Milan, 20133, Milan, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy.
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Millet CP, Allinne C, Vi T, Marraccini P, Verleysen L, Couderc M, Ruttink T, Zhang D, Sanchéz WS, Tranchant-Dubreuil C, Jeune W, Poncet V. Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity. PLoS One 2024; 19:e0299493. [PMID: 38625928 PMCID: PMC11020479 DOI: 10.1371/journal.pone.0299493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/11/2024] [Indexed: 04/18/2024] Open
Abstract
Though facing significant challenges, coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. However, little is known about their genetic diversity and the variety mixtures used. In light of this, there is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 diverse farms in historically important coffee growing regions of northern and southern Haiti. We performed KASP-genotyping of SNP markers and HiPlex multiplex amplicon sequencing for haplotype calling on our samples, as well as several Ethiopian and commercial accessions from international collections. This allowed us to assign Haitian samples to varietal groups. Our analyses revealed considerable genetic diversity in Haitian farms, higher in fact than many farmers realized. Notably, genetic structure analyses revealed the presence of clusters related to Typica, Bourbon, and Catimor groups, another group that was not represented in our reference accession panel, and several admixed individuals. Across the study areas, we found both mixed-variety farms and monovarietal farms with the historical and traditional Typica variety. This study is, to our knowledge, the first to genetically characterize Haitian C. arabica variety mixtures, and report the limited cultivation of C. canephora (Robusta coffee) in the study area. Our results show that some coffee farms are repositories of historical, widely-abandoned varieties while others are generators of new diversity through genetic mixing.
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Affiliation(s)
- Claude Patrick Millet
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- Faculté des Sciences de l’Agriculture et de l’Environnement, Université de Quisqueya, Port-au-Prince, Haiti
- Institut Agro, ABSys, Université Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ABSys, F-34398, Montpellier, France
| | - Clémentine Allinne
- Institut Agro, ABSys, Université Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ABSys, F-34398, Montpellier, France
- GECO, Université Montpellier, CIRAD, Montpellier, France
- CIRAD, UPR GECO, F-34398, Montpellier, France
| | - Tram Vi
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Pierre Marraccini
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- CIRAD, UMR DIADE, Montpellier, France
| | - Lauren Verleysen
- Faculty of Sciences, Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- ILVO, Melle, Belgium
| | - Marie Couderc
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
| | - Tom Ruttink
- ILVO, Melle, Belgium
- Ghent University, Ghent, Belgium
| | - Dapeng Zhang
- USDA-ARS, SPCL, Beltsville, Maryland, United States of America
| | | | | | - Wesly Jeune
- Faculté des Sciences de l’Agriculture et de l’Environnement, Université de Quisqueya, Port-au-Prince, Haiti
- AVSF, Pétion-Ville, Haïti
| | - Valérie Poncet
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
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Ochoa-Aristizábal AM, Márquez EJ. Genetic insights into Cyphocharax magdalenae (Characiformes: Curimatidae): Microsatellite loci development and population analysis in the Cauca River, Colombia. PLoS One 2024; 19:e0302273. [PMID: 38625982 PMCID: PMC11020439 DOI: 10.1371/journal.pone.0302273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/29/2024] [Indexed: 04/18/2024] Open
Abstract
Cyphocharax magdalenae, a Colombian freshwater fish species, plays a vital role in nutrients distribution and serves as a significant food source for other fish species and local fishing communities. Considered a short-distance migratory species, C. magdalenae populations face substantial extinction risk due to human activities impacting their habitats. To address the lack of knowledge on genetic diversity and population structure, this study used next-generation sequencing technology to develop species-specific microsatellite loci and conducted a population genetics analysis of C. magdalenae in the middle and lower sections of the Cauca River, Colombia. Out of 30 pairs of microsatellite primers evaluated in 324 individuals, 14 loci were found to be polymorphic, at linkage equilibrium and, in at least one population, their genotypic frequencies were in Hardy-Weinberg equilibrium. Results showed high genetic diversity levels compared to other neotropical Characiformes, with inbreeding coefficients similar to those reported for phylogenetically related species. Moreover, C. magdalenae exhibits seasonal population structure (rainy-dry) consisting of two genetic stocks showing bottleneck signals and high effective population sizes. This information is essential for understanding the current species genetics and developing future management programs for this fishery resource.
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Affiliation(s)
- Ana Maria Ochoa-Aristizábal
- Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Facultad de Ciencias Universidad Nacional de Colombia – Sede Medellín, Medellín, Antioquia, Colombia
| | - Edna Judith Márquez
- Laboratorio de Biología Molecular y Celular, Escuela de Biociencias, Facultad de Ciencias Universidad Nacional de Colombia – Sede Medellín, Medellín, Antioquia, Colombia
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50
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Qu F, Khemsom K, Perdoncini Carvalho C, Han J. Quasispecies are constantly selected through virus-encoded intracellular reproductive population bottlenecking. J Virol 2024; 98:e0002024. [PMID: 38445885 PMCID: PMC11019954 DOI: 10.1128/jvi.00020-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Affiliation(s)
- Feng Qu
- Department of Plant Pathology, The Ohio State University Wooster Campus, Wooster, Ohio, USA
| | - Khwannarin Khemsom
- Department of Plant Pathology, The Ohio State University Wooster Campus, Wooster, Ohio, USA
| | | | - Junping Han
- Department of Plant Pathology, The Ohio State University Wooster Campus, Wooster, Ohio, USA
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