Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control

Bananas (Musa spp.) are one of the world’s most important fruit crops, and play a vital role for food security in many developing countries. Most of banana cultivars are triploids derived after inter- and intra-specific hybridizations of the wild diploid ancestor species Musa acuminate (AA) and M. balbisiana (BB). Here, we report two haplotype-resolved genome assemblies of representative AAB cultivated types (Plantain and Silk) and precisely characterize ancestral contributions by examining ancestry mosaics across the genome. Widespread asymmetric evolution is observed in their subgenomes, which could be linked to frequent homologous exchange (HE) events. We reveal the genetic makeup of triploid banana cultivars and verify that subgenome B is a rich source of resistance genes. Only 58.5% and 59.4% of Plantain and Silk genes are present in all three haplotypes, with >50% of genes including differentially expressed alleles in different subgenomes. We observe that the number of up-regulated genes in Plantain is significantly higher than that in Silk at one weeks postinoculation following banana Fusarium wilt tropical race 4 (Foc TR4) infection, confirming that Plantain can initiate defense responses more quickly. In addition, we analyze the genetics and expression difference of genes related to carotenoid synthesis and starch metabolism between Plantain and Silk. Our study provides resources for better understanding the genomic architecture of cultivated bananas and has important implications for Musa genetics and breeding.