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

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.