دورية أكاديمية
Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors
| العنوان: | Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors |
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| المؤلفون: | Campbell, Lahcen, I., Nwezeobi, Joachim, van Brunschot, Sharon, L., Kaweesi, Tadeo, Seal, Susan, E., Swamy, Rekha, A. R., Namuddu, Annet, Maslen, Gareth, L., Mugerwa, Habibu, Armean, Irina, M., Haggerty, Leanne, Martin, Fergal, J., Malka, Osnat, Santos-Garcia, Diego, Juravel, Ksenia, Morin, Shai, Stephens, Michael, E., Muhindira, Paul, Visendi, Kersey, Paul, J., Maruthi, M., N., Omongo, Christopher, A., Navas-Castillo, Jesús, Fiallo-Olivé, Elvira, Mohammed, Ibrahim, Umar, Wang, Hua-Ling, Onyeka, Joseph, Alicai, Titus, Colvin, John |
| المساهمون: | European Bioinformatics Institute Hinxton (EMBL-EBI), EMBL Heidelberg, Natural Resources Institute Chatham, University of Greenwich, The Wellcome Trust Sanger Institute Cambridge, School of Biological Sciences Brisbane, The University of Queensland (UQ All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations ), CSIRO Health and Biosecurity Australia, Commonwealth Scientific and Industrial Research Organisation Canberra (CSIRO), National Crops Resources Research Institute (NaCRRI), Kampala, Uganda, University of Georgia USA, The Hebrew University of Jerusalem (HUJ), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Cornell University New York, Institute for Molecular Bioscience, Royal Botanic Gardens Kew, Instituto de Hortofruticultura Subtropical y Mediterranea "La Mayora" (IHSM), Consejo Superior de Investigaciones Cientificas España = Spanish National Research Council Spain (CSIC)-Universidad de Málaga Málaga = University of Málaga Málaga, Kebbi State University of Science and Technology (KSUSTA), Agricultural University of Hebei, National Root Crops Research Institute (NRCRI), Umudike, Abia State, Nigeria, This work was supported, in whole or in part, by the Bill & Melinda Gates Foundation Grant Numbers OPP1058938, INV-010435 (previously OPP1200124) and OPP1149777 . Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. SVB was funded in part by the Cotton Research and Development Corporation (Australia, Grant Number UQ1305). LH and FJM were funded by the Wellcome Trust WT108749/Z/15/Z, WT222155/Z/20/Z . |
| المصدر: | ISSN: 1471-2164 ; BMC Genomics ; https://hal.inrae.fr/hal-04182772Test ; BMC Genomics, 2023, 24, pp.408. ⟨10.1186/s12864-023-09474-3⟩ ; https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09474-3Test. |
| بيانات النشر: | HAL CCSD BioMed Central |
| سنة النشر: | 2023 |
| المجموعة: | HAL Lyon 1 (University Claude Bernard Lyon 1) |
| مصطلحات موضوعية: | Biological species, Genome assembly, Comparative genomics, Phylogenomics, Cladogenesis, Transposons, Endosymbiont, Horizontal genes, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] |
| الوصف: | The genomes, transcriptomes, and predicted protein-coding sequences are available from Ensembl Metazoa (http://metazoa.ensembl.orgTest) and are included within the references. Raw RNA-Seq datasets generated and/or analyzed during the current study are available from the European Nucleotide Archive database repository (https://www.ebi.ac.uk/enaTest) under the parent project accessions: PRJEB28507, PRJEB36965, PRJEB35304, PRJEB39408. All data generated during the analyses of these datasets are included in this published article, supplementary information files, and figshare repository (https://doi.org/10.6084/m9.figshare.23666799Test; https://doi.org/10.6084/m9.figshare.23666832.v4Test; https://doi.org/10.6084/m9.figshare.23666844Test). ; International audience ; Background: The group of > 40 cryptic whitefly species called Bemisia tabaci sensu lato are amongst the world's worst agricultural pests and plant-virus vectors. Outbreaks of B. tabaci s.l. and the associated plant-virus diseases continue to contribute to global food insecurity and social instability, particularly in sub-Saharan Africa and Asia. Published B. tabaci s.l. genomes have limited use for studying African cassava B. tabaci SSA1 species, due to the high genetic divergences between them. Genomic annotations presented here were performed using the 'Ensembl gene annotation system' , to ensure that comparative analyses and conclusions reflect biological differences, as opposed to arising from different methodologies underpinning transcript model identification. Results: We present here six new B. tabaci s.l. genomes from Africa and Asia, and two re-annotated previously published genomes, to provide evolutionary insights into these globally distributed pests. Genome sizes ranged between 616-658 Mb and exhibited some of the highest coverage of transposable elements reported within Arthropoda. Many fewer total protein coding genes (PCG) were recovered compared to the previously published B. tabaci s.l. genomes and structural annotations generated via the uniform ... |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| العلاقة: | info:eu-repo/semantics/altIdentifier/pmid/37468834; hal-04182772; https://hal.inrae.fr/hal-04182772Test; https://hal.inrae.fr/hal-04182772/documentTest; https://hal.inrae.fr/hal-04182772/file/s12864-023-09474-3.pdfTest; PUBMED: 37468834; WOS: 001032102600003 |
| DOI: | 10.1186/s12864-023-09474-3 |
| الإتاحة: | https://doi.org/10.1186/s12864-023-09474-3Test https://hal.inrae.fr/hal-04182772Test https://hal.inrae.fr/hal-04182772/documentTest https://hal.inrae.fr/hal-04182772/file/s12864-023-09474-3.pdfTest |
| حقوق: | http://creativecommons.org/licenses/by-ncTest/ ; info:eu-repo/semantics/OpenAccess |
| رقم الانضمام: | edsbas.B0D816A6 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1186/s12864-023-09474-3 |
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