Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors
Martin, Guillaume | Istace, Benjamin | Baurens, Franc-Christophe | Belser, Caroline | Hervouet, Catherine | Labadie, Karine | Cruaud, Corinne | Noel, Benjamin | Guiougou, Chantal | Salmon, Frédéric | Mahadeo, Joël | Ahmad, Fajarudin | Volkaert, Hugo, A. | Droc, Gaëtan | Rouard, Mathieu | Sardos, Julie | Wincker, Patrick | Yahiaoui, Nabila | Aury, Jean-Marc | D’hont, Angélique | Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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) | Génomique métabolique (UMR 8030) ; Genoscope - Centre national de séquençage [Evry] (GENOSCOPE) ; Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) | Département Systèmes Biologiques (Cirad-BIOS) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad) | Genoscope - Centre national de séquençage [Evry] (GENOSCOPE) ; Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) | National Research and Innovation Agency (BRIN) | Kasetsart University [Bangkok, Thailand] (KU) | Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE) ; Ministry of Education Thaïland | The Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT) [France] ; Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance) ; Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR) | This research was supported by the Genoscope, the French Alternative Energies and Atomic Energy Commission (CEA), France Génomique (ANR-10-INBS-0009, DYNAMO project), the Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), and the Agropolis Fondation (ID 1504-006). GenomeHarvest project through the French Investissements d’Avenir program (Labex Agro: ANR-10-LABX-0001). We thank CIRAD-INRAE Biological Resource Centre for Tropical Plants (CRB-PT) in the West Indies (Guadeloupe, France) for providing the plant materials. This work was technically supported by the CIRAD—UMR AGAP HPC Data Center of the South Green Bioinformatics platform. | CIRAD—UMR AGAP HPC Data Center of the South Green Bioinformatics platform, Montpellier, France | CIRAD-INRAE Biological Resource Centre for Tropical Plants (CRB-PT) in the West Indies, Guadeloupe, France | ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010) | ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Data availability: The Illumina, ONT, PACBIO HiFi, Bionano Genomics, Hi-C data, assemblies and annotations generated in this study have been deposited in the European Nucleotide Archive under project PRJEB72282. The genome assemblies and gene and TE annotations are available at Banana Genome Hub [http://banana-genome-hub.southgreen.fr]. GBSS and ADH alignments, EDTA repeat database and LTR repeat database produced are available on the Banana Genome Hub [http://banana-genome-hub.southgreen.fr] in the download section and on CIRAD dataverse [https://doi.org/10.18167/DVN1/6TLMD3]. The GBS data are available in the Short Read Archive under the following projects PRJNA1078411, PRJNA1182927 and PRJNA667853. Germplasm is available at the CIRAD-INRAE Biological Resource Centre for Tropical Plants (CRB-PT) in the West Indies (Guadeloupe, France) for accessions PT-BA-00024 (M. a. ssp. banksii); PT-BA-00228 for M. textilis; PT-BA-00182 for M. a. ssp. zebrina; PT-BA-00051 for M. a. ssp. burmannicoides and PT-BA-00304 for the diploid cultivated Pisang Madu. Germplasm of M. schizocarpa is available at the Bioversity International Transit Center in Leuven (Belgium) under ITC0926 accession number. Publicly available sequencing data (PRJEB58004 [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB58004] and PRJEB26661) were also used in this study. Source data are provided with this paper.Code availability: Custom code has been added to vcfHunter toolbox that is available at Github [https://github.com/SouthGreenPlatform/VcfHunter].
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Показать больше [+] Меньше [-]Английский. Hybridization between wild Musa species and subspecies from Southeast Asia is at the origin of cultivated bananas. The genomes of these cultivars are complex mosaics involving nine genetic groups, including two previously unknown contributors. This study provides continuous genome assemblies for six wild genetic groups, one of which represents one of the unknown ancestor, identified as M. acuminata ssp. halabanensis. The second unknown ancestor partially present in a seventh assembly appears related to M. a. ssp. zebrina. These assemblies provide key resources for banana genetics and for improving cultivar assemblies, including that of the emblematic triploid Cavendish. Comparative and phylogenetic analyses reveal an ongoing speciation process within Musa, characterised by large chromosome rearrangements and centromere differentiation through the integration of different types of repeated sequences, including rDNA tandem repeats. This speciation process may have been favoured by reproductive isolation related to the particular context of climate and land connectivity fluctuations in the Southeast Asian region.
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