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Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

2018; University of Oxford; Volume: 7; Issue: 5 Linguagem: Inglês

10.1093/gigascience/giy044

2047-217X

Chien‐Yueh Lee, Ping‐Han Hsieh, Li-Mei Chiang, Amrita Chattopadhyay, Kuanyi Li, Yi-Fang Lee, Tzu‐Pin Lu, Liang‐Chuan Lai, En-Chung Lin, Hsinyu Lee, Shih‐Torng Ding, Mong‐Hsun Tsai, Chien‐Yu Chen, Eric Y. Chuang,

Aquaculture disease management and microbiota

Abstract Background The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear. Results We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago. Conclusions This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.