1. Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant
- Author
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Hsinyu Lee, Kuan-Yi Li, Shih-Torng Ding, Tzu-Pin Lu, Eric Y. Chuang, Liang-Chuan Lai, Ping-Han Hsieh, En-Chung Lin, Mong-Hsun Tsai, Yi-Fang Lee, Chien-Yu Chen, Chien-Yueh Lee, Amrita Chattopadhyay, and Li-Mei Chiang
- Subjects
0301 basic medicine ,Hemoglobin binding ,Mikado pheasant ,Health Informatics ,long-tailed pheasant ,Pheasant ,Evolution, Molecular ,Major Histocompatibility Complex ,Contig Mapping ,Hemoglobins ,Open Reading Frames ,03 medical and health sciences ,0302 clinical medicine ,Species Specificity ,Molecular evolution ,biology.animal ,Animals ,Galliformes ,Selection, Genetic ,Phylogeny ,Synteny ,Syrmaticus ,adaptive evolution ,Genome ,Whole Genome Sequencing ,biology ,Research ,Oxygen transport ,Syrmaticus mikado ,food and beverages ,Molecular Sequence Annotation ,DNA ,de novo genome assembly ,biology.organism_classification ,Adaptation, Physiological ,Computer Science Applications ,030104 developmental biology ,Amino Acid Substitution ,whole-genome sequencing ,Evolutionary biology ,Multigene Family ,Female ,Chickens ,030217 neurology & neurosurgery - 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.
- Published
- 2018
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