Pioneering Whole-Genome Sequencing of the Mikado Pheasant in Taiwan
The Mikado pheasant indigenous to Taiwan has not only been classified as a nearly threatened species by the International Union for Conservation of Nature Red List, it is also one of the protected wild animals in Taiwan. Because of its extreme rarity, this bird species has attracted much attention and observation. Under the support of NTU, the Ministry of Science and Technology (MOST), and Taipei Zoo, an NTU cross-disciplinary team led by Prof. Eric Y. Chuang (莊曜宇), Director of NTU’s Graduate Institute of Biomedical Electronics and Bioinformatics, has conducted the world’s first whole-genome sequencing of the Mikado pheasant. The team’s findings were published in GigaScience under the title, Whole-Genome de novo Sequencing Reveals Unique Genes that Contributed to the Adaptive Evolution of the Mikado Pheasant. The study provides valuable insights into the Mikado pheasant’s adaptation to high altitude and the evolutionary history of the genus Syrmaticus, which are potentially useful for future studies on molecular evolution, genomics, ecology, and immunogenetics.
The Mikado pheasant, indigenous and peculiar to Taiwan, is the island’s largest pheasant inhabiting in mountainous regions at very high elevations, and its image is printed on the back of the NT$1000 bill. Due to hunting pressure, the pheasant faced endangerment along with a decreasing population. The NTU team presented the pheasant’s draft genome, which consisted of 1.04 Gb of DNA and nearly 16,000 annotated protein-coding genes. The team found that the pheasant’s exceptional adaption to high-altitude environments could have been attributed to the expansion and positive selection of genes related to features including energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. By completing a whole-genome de novo sequencing of the Mikado pheasant and performing a molecular clock analysis, the team suggested that ancestors of the Mikado pheasant might have migrated to Taiwan about 3.47 million years ago, an estimation supported by paleogeographical studies for its temporal coincidence with the formation of the Taiwan Island. The major histocompatibility complex B-locus (MHC-B) genes are a crucial cluster of immune genes for avian species. The team identified that the Mikado pheasant and the chicken share a similar genetic MHC-B region and a nearly perfect syntenic gene order. These findings provide valuable clues and resources for future studies on bird flu prevention and treatment.
Genomic mapping is a new, effective, and widely used method for preserving and utilizing important biological resources. By interpreting the Mikado pheasant’s genetic atlas, this study provides a means to permanently preserve the biological data of avian species and to identify the species-specific characteristics required for conservation, thus revealing the association between the Mikado pheasant’s genes and properties (e.g., evolution and environmental adaptation). The completion of this research project not only marks a new milestone in Taiwan’s ecological conservation efforts, but also enhances academic collaborations and Taiwan’s international visibility.
Prof. Eric Y. Chuang (莊曜宇)
NTU Graduate Institute of Biomedical Electronics and Bioinformatics