Bananas (Musa ssp.) are a major staple crop and fruit that feeds millions of people every day. Triploid bananas are the predominant cultivars, including Plantains (AAB genome) and Cavendish (AAA). Most fresh bananas belong to the Cavendish, which is the most important cultivar.

Cavendish 

Before Cavendish bananas became so popular, the Gros Michel cultivar was the most popular type of banana. The fungal pathogen F. oxysporum f. sp. cubense (Foc) race 1 has led to the near complete replacement of Gros Michel with Cavendish, which is resistant to Foc race 1. The Foc tropical race 4 (TR4) disease now seriously threatens Cavendish bananas. However, no triploid banana reference genome has been reported.

To further our understanding of these triploid banana genomes, and to be able to better preserve them for the future, we here report the high-quality chromosome-scale genome assemblies of the Cavendish (AAA, 1.48 Gb) and Gros Michel (AAA, 1.32 Gb) subgroups. We defined three sub-genomes and identify their ancestors as M. acuminata ssp. banksii, zebrina and malaccensis for cultivated bananas. Comparative analyses of the Fusarium wilt pathogens Foc TR4 and Foc race 1 resistance genes using our high-quality AAA reference genomes indicates that insertion of repeat sequences in the RGA2 promoter of Cavendish and Gros Michel likely result in insufficient expression of endogenous RGA2 to confer Foc TR4 protection. The loss of the RLP locus in the Gros Michel Ze sub-genome leads to the loss of key resistance genes to Foc race 1, explaining the susceptibility of Gros Michel to Foc race 1. 

We also identified two novel NAP homologs specifically highly expressed in fruit. ChIP-Seq analysis reveals these NAPs being able to bind to the promoters of many fruit ripening genes, and are critical for fruit ripening. In combination with these genes that are highly expressed in ripe fruit tissues, we can identify many new ripening-related genes, making them candidates for the improvement of fruit quality traits.   

The triploid banana genome unveils the banana cultivars' origins, disease resistance and fruit ripening mechanism. We believe that our two high-quality triploid AAA genome assemblies will serve as future references for functional genomics and comparative genome analyses to identify, clone and characterize genes responsible for important agronomic traits, including fruit quality and disease resistance, such as Foc TR4 disease. These data should serve as a platform for future evolutionary studies and will facilitate molecular breeding and super-domestication of bananas.

Most cultivated crops have been sequenced and entered the genomic era. But the genomes of some important cultivars have not yet been sequenced, such as cultivated bananas, modern roses and lily. We report here on cultivated banana genomes, which will advance the annotation of functional elements of bananas in the post-genomic era.