The pangenome of banana highlights differences between genera and genomes.

Habib Rijzaani,Jacqueline Batley,Mathieu Rouard,Jaroslav Doležel,Philipp E Bayer,David Edwards

doi:10.1002/tpg2.20100

Abstract

Banana (Musaceae family) has a complex genetic history and includes a genus Musa with a variety of cultivated clones with edible fruits, Ensete species that are grown for their edible corm, and monospecific Musella whose generic status has been questioned. The most commonly exported banana cultivars belong to Cavendish, a subgroup of Musa triploid cultivars, which is under threat by fungal pathogens, though there are also related species M. balbisiana Colla (B genome), M. textilis Née (T genome), and M. schizocarpa N. W. Simmonds (S genome), along with hybrids of these genomes, which potentially host genes of agronomic interest. Here we present the first cross-genus pangenome of banana, which contains representatives of the Musa and Ensete genera. Clusters based on gene presence-absence variation (PAV) clearly separate Musa and Ensete, while Musa is split further based on species. These results present the first pangenome study across genus boundaries and identifies genes that differentiate between Musaceae species, information that may support breeding programs in these crops.

Highlights

The banana family (Musaceae) is a monophyletic clade comprising of three genera, Musa, Ensete, and Musella (Kress, Abbreviations: Benchmarking universal single-copy orthologs (BUSCO), benchmarking universal single-copy orthologs; Gene ontology (GO), gene ontology; nucleotide bindingsite leucine rich repeat (NLR), nucleotide binding-site leucine rich repeat; presence–absence variations (PAVs), presence–absence variation; resistance gene analogs (RGAs), resistance gene analog; SNP, single nucleotide polymorphism.1990)
Most of the identified species of this family belong to the Musa genus, which includes the edible fruit-bearing banana cultivars, with the latest database of Musa Germplasm Information System recording 6,548 accessions that are maintained in 29 collections around the world (Ruas et al, 2017)
We have assembled the first pangenome of the banana family (Musaceae) using the iterative mapping and assembly approach (Golicz et al, 2016), representing three Musa species, a diverse group of cultivated banana clones and one Ensete species

Summary

Introduction

The banana family (Musaceae) is a monophyletic clade comprising of three genera, Musa, Ensete, and Musella (Kress, Abbreviations: BUSCO, benchmarking universal single-copy orthologs; GO, gene ontology; NLR, nucleotide binding-site leucine rich repeat; PAV, presence–absence variation; RGA, resistance gene analog; SNP, single nucleotide polymorphism.1990). We produced a draft cross-genus pangenome that captures the diversity of banana genome types and highlights the diversity of gene content across the Musaceae, identifying genes that may play a role in the evolutionary differentiation between Ensete and Musa genera as well as variable genes that could be used to improve the agronomic performance and disease resistance in this important family.

Results

Conclusion