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Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.

Musa banksii is a species of wild banana in the genus Musa, native to New Guinea, Manus, northern Australia and some islands of eastern Indonesia. In this study, the chloroplast genome sequence of M. banksii been assembled and characterized by Illumina sequencing. The complete chloroplast genome was 170,010 bp in length, containing a large single copy region (LSC) of 88,373 bp and a small single copy region (SSC) of 10,769 bp, which were separated by a pair of 35,434 bp inverted repeat regions (IRs). A total of 136 genes were predicted, including 113 unique genes consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Maximum-likelihood phylogenetic analysis of 11 representative plastomes within the order Zingiberales suggests that M. banksii closely related to the Musa ornata and Musa acuminata.