Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat

Abstract

Background The Hengduan Mountains, one of the global biodiversity hotspots with exceptional species richness and high endemism, contains numerous arid valleys that create a distinctive geographical and ecological landscape. However, the adaptive evolutionary mechanisms of organism in the arid valley remain poorly understood. Minois aurata , an endemic butterfly species found exclusively in the arid valley of the upper Minjiang River, represents an attractive model system for studying adaptive evolutionary mechanisms to arid valley environments. Results Here, we present the first chromosome-level genome assembly for Minois aurata , with a total size of approximately 609.17 Mb, and a scaffold N50 size of 23.88 Mb. These scaffolds were further clustered and anchored onto 29 chromosomes based on Hi-C data. A total of 16,163 protein-coding genes were predicted, of which 91.83% were functionally annotated. The expansion of transposable elements (TEs) accounts for the relatively large genome size of M. aurata , potentially aiding its adaptation to environmental conditions. Phylogenomic analyses based on 3,785 single-copy genes revealed that M. aurata is most closely related to Hipparchia semele . Further mitochondrial genome analysis of four Minois species placed M. aurata in a basal position within the genus, supporting it as an independent species. A total of 185 rapidly evolving and 232 specific gene families were identified in M. aurata . Functional enrichment analysis indicated that these gene families were mainly associated with ultraviolet radiation, heat and hypoxia responses. We also identified 234 positive selected genes in M. aurata , some of which are related to compound eye photoreceptor development, osmotic stress, and light stimulus response. Demographic analysis indicated that the effective population size of M. aurata decreased around 0.4 and 0.04 million years ago, respectively, coinciding with the localized sub-glaciation. Conclusion The chromosome-level genome offers a comprehensive genomic basis for understanding the evolutionary and adaptive strategies of Minois aurata in the unique arid valley environment of the Hengduan Mountains, while also providing valuable insights into the broader mechanisms of organism adaptation to such habitats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-024-11058-8.