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The draft genome of the blood pheasant (Ithaginis cruentus): phylogeny and high-altitude adaptation

Citation

Chuang, Zhou (2021), The draft genome of the blood pheasant (Ithaginis cruentus): phylogeny and high-altitude adaptation, Dryad, Dataset, https://doi.org/10.5061/dryad.g79cnp5mb

Abstract

The blood pheasant (Ithaginis cruentus), the only species in the genus Ithaginis lives in an extremely inhospitable high-altitude environment, coping with hypoxia and UV radiation. To further investigate the phylogeny of Phasianidae species based on complete genomes and understand the molecular genetic mechanisms of the high-altitude adaptation of the blood pheasant, we de novo assembled and annotated the complete genome of the blood pheasant. The blood pheasant genome size is 1.04 Gb with scaf N50 of 10.88 Mb. We identified 109.92 Mb (10.62%) repeat elements, 279,037 perfect SSR and 17,209 protein-coding genes. The largest phylogenetic tree on the basis of whole genomes revealed three major clades of the Phasianidae with strong support, which the blood pheasant was included in the “erectile clade”. Comparative genomics analysis showed that many genes were positively selected in the blood pheasant, which was associated with response to hypoxia and/or ultraviolet (UV) radiation. More importantly, among these positively selected genes (PSGs) which were related to high-altitude adaptation, sixteen PSGs had blood pheasant-specific missense mutations. Our data and analysis laid solid foundation to the study of Phasianidae phylogeny and provided new insights into the potential adaptation mechanisms to the high altitude employed by the blood pheasant.

Funding

National Natural Science Foundation of China, Award: 3,170,201,731,970,390