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

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.

Molecular Basis of Disease Resistance in Banana Progenitor Musa balbisiana against Xanthomonas campestris pv. musacearum

“…This genome sequence is considered to be the reference genome for Musa species due to its completeness and quality of annotation 58 . The quality of annotation has recently been quantified through a BUSCO analysis, which scores the genome of Musa acuminata DH Pahang at 96.5% and the genome of Musa balbisiana Pisang Klutuk Wulung at 66.5% 59 . This genome sequence has been extensively used in other transcriptome studies on Musa including genotypes having B-genome 60 .…”

The Timing and Direction of Introgression Under the Multispecies Network Coalescent

“…We have also introduced the D 2 statistic for distinguishing the direction of introgression between two taxa [see Rouard et al (2018) for an empirical example using this test]. Despite the importance of understanding the direction of gene flow, relatively few studies have explicitly attempted to provide a solution to the problem when only a single sequence is sampled from each lineage.…”

Chromosome painting in cultivated banana and their wild relatives (Musaspp.) reveals differences in chromosome structure

“…Based on morphology and geographical distribution, M. acuminata has been divided into nine subspecies (banksii, burmannica, burmannicoides, errans, malaccensis, microcarpa, siamea, truncata and zebrina) and three varieties (chinensis, sumatrana, tomentosa) (Perrier et al, 2011, Martin et al, 2017, WCSP, 2018. It has been estimated that least four subspecies of M. acuminata contributed to the origin of cultivated bananas (Perrier et al, 2011, Rouard et al, 2018. Out of them, M. acuminata ssp.…”

“…malaccensis with the origin in Malay peninsula (De Langhe et al, 2009, Perrier et al, 2011 and ssp. zebrina which originated in Indonesia (Rouard et al, 2018).…”