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Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)

Rouard Mathieu, Droc Gaëtan, Martin Guillaume, Sardos Julie, Hueber Yann, Guignon Valentin, Cenci Alberto, Geigle B., Hibbins M.S., Yahiaoui Nabila, Baurens Franc-Christophe, Berry V., Hahn M.W., D'Hont Angélique, Roux Nicolas. 2018. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biology and Evolution, 10 (12) : pp. 3129-3140.

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Quartile : Q2, Sujet : GENETICS & HEREDITY / Quartile : Q2, Sujet : EVOLUTIONARY BIOLOGY

Abstract : Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.

Mots-clés Agrovoc : Musa acuminata, Musa balbisiana, Génome, Phylogénie, Hybridation

Mots-clés géographiques Agrovoc : Asie du Sud-Est, Chine, Malaisie, Indonésie

Mots-clés libres : Banana, Musa, Incomplete lineage sorting, Phylogenomics, Assembly

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Rouard Mathieu, Bioversity International (FRA) - auteur correspondant
  • Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)
  • Martin Guillaume, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-1801-7500
  • Sardos Julie, Bioversity International (FRA)
  • Hueber Yann, Bioversity International (ITA)
  • Guignon Valentin, Bioversity International (FRA)
  • Cenci Alberto, Bioversity International (ITA)
  • Geigle B., Bioversity International (FRA)
  • Hibbins M.S., Indiana University (IND)
  • Yahiaoui Nabila, CIRAD-BIOS-UMR AGAP (FRA)
  • Baurens Franc-Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-5219-8771
  • Berry V., CNRS (FRA)
  • Hahn M.W., Indiana University (IND)
  • D'Hont Angélique, CIRAD-BIOS-UMR AGAP (FRA)
  • Roux Nicolas, Bioversity International (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/589366/)

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