PT  - JOURNAL ARTICLE
AU  - M Rouard
AU  - G Droc
AU  - G Martin
AU  - J Sardos
AU  - Y Hueber
AU  - V Guignon
AU  - A Cenci
AU  - B Geigle
AU  - M S Hibbins
AU  - N Yahiaoui
AU  - F-C Baurens
AU  - V Berry
AU  - M W Hahn
AU  - A D’Hont
AU  - N Roux
TI  - Three new genome assemblies support a rapid radiation in <em>Musa acuminata</em> (wild banana)
AID  - 10.1101/306605
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 306605
4099  - http://biorxiv.org/content/early/2018/04/26/306605.short
4100  - http://biorxiv.org/content/early/2018/04/26/306605.full
AB  - 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 and genome evolution. 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 a substantial portion of the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support future evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.