Genome Assembly and Multi-Omics Analysis of Musa cheesmanii: Unveiling Banana Evolution and Pseudo-Stem Pigmentation

Genomic insights into the diversification and origin of the Musa species are of great significance for developing new banana cultivars (Musa spp.). In the genus, Musa cheesmanii is a remarkable wild species with an interesting taxonomic position within the clade of species that have contributed to most cultivated bananas, although it was not, however, very well characterized and remains understudied. We reported its genome in a telomere-to-telomere (T2T) gap-free reference genome. The genome size was estimated to be 432.16 Mb, with 41.96% of repetitive sequences, making it one of the most compact genomes in the genus Musa. Phylogenetic analysis of M. cheesmanii and banana progenitor species based on 9,388 single-copy genes grouped the sect. Musa into two clades: clade A, containing Musa acuminata and Musa schizocarpa, and clade B, including M. cheesmanii and Musa balbisiana. The inversion on chromosome 5 occurred independently in clade A, while the large reciprocal translocation between chromosomes 1 and 3 was found only in M. balbisiana. These two clades displayed different demographic history with an effective population size of clade B species decreasing gently after the Naynayxungla Glaciation (0.50-0.78 Myr ago), while clade A species experienced a dramatic decline around the Penultimate Glaciation (135-194 kyr ago). Four key genes involved in anthocyanin biosynthesis showed higher expression in the pseudo-stem of M. cheesmanii, potentially accounting for its distinctive black color. Furthermore, different classes of anthocyanin compounds, present in high abundance in the pseudo-stem of M. cheesmanii, were detected, which generally contributed to cope with abiotic and biotic stress. These findings shed light on the evolution of the Musa genus and the molecular underpinnings of pseudo-stem coloration, which could serve as an important genomic resource for horticultural and stress-resistant banana breeding.