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Crop wild relatives are valuable resources for future genetic improvement. Here, we report the  de novo  genome assembly of  Musa itinerans , a disease-resistant wild banana relative in subtropical China. The assembled genome size was 462.1 Mb, covering 75.2% of the genome (615.2Mb) and containing 32, 456 predicted protein-coding genes. Since the approximate divergence around 5.8 million years ago, the genomes of  Musa itinerans  and  Musa acuminata  have shown conserved collinearity. Gene family expansions and contractions enrichment analysis revealed that some pathways were associated with phenotypic or physiological innovations. These include a transition from wood to herbaceous in the ancestral Musaceae, intensification of cold and drought tolerances, and reduced diseases resistance genes for subtropical marginally distributed  Musa  species. Prevalent purifying selection and transposed duplications were found to facilitate the diversification of NBS-encoding gene families for two  Musa  species. The population genome history analysis of  M. itinerans  revealed that the fluctuated population sizes were caused by the Pleistocene climate oscillations, and that the formation of Qiongzhou Strait might facilitate the population downsizing on the isolated Hainan Island about 10.3 Kya. The qualified assembly of the  M. itinerans  genome provides deep insights into the lineage-specific diversification and also valuable resources for future banana breeding.

Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus