Supporting data for "Whole-Genome De Novo Sequencing Reveals Unique Genes that Contributed to the Adaptive Evolution of the Mikado Pheasant"

Dataset type: Genomic
Data released on April 05, 2018

Lee CY; Hsieh PH; Chiang LM; Chattopadhyay A; Li KY; Lee YF; Lu TP; Lai LC; Lin EC; Lee H; Ding ST; Tsai MH; Chen CY; Chuang EY (2018): Supporting data for "Whole-Genome De Novo Sequencing Reveals Unique Genes that Contributed to the Adaptive Evolution of the Mikado Pheasant" GigaScience Database. http://dx.doi.org/10.5524/100431

DOI10.5524/100431

The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. It possesses a unique position in evolution because of its geographic isolation. Currently, the genetic background and adaptive behaviors of the Mikado pheasant remain unclear.
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. The major histocompatibility complex (MHC) region contains 39 putative genes within 227 kb of DNA. Compared with the chicken MHC, we not only found that TAPBP and the TAP1-TAP2 block are in inverse orientation, but also identified some genes undergoing rapid evolution. The complete mitochondrial genome was further sequenced, assembled, and compared against 4 other 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.
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 investigating molecular evolution, genomics, and immunogenetics.

Additional details

Read the peer-reviewed publication(s):

Lee, C.-Y., Hsieh, P.-H., Chiang, L.-M., Chattopadhyay, A., Li, K.-Y., Lee, Y.-F., … Chuang, E. Y. (2018). Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. GigaScience, 7(5). doi:10.1093/gigascience/giy044

Accessions (data included in GigaDB):

BioProject: PRJNA389983
SRA: SRP108966





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
N19065 Mikado pheasantSyrmaticus mikado Description:DNA extracted from the blood of a sing...
Analyte type:DNA
Sex:Female
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N29065 Mikado pheasantSyrmaticus mikado Description:RNA extracted from the blood of a sing...
Alternative names:RNA-RF-185
Analyte type:RNA
...
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N39065 Mikado pheasantSyrmaticus mikado Description:RNA extracted from the blood of a sing...
Alternative names:RNA-RF-165
Analyte type:RNA
...
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Displaying 1-3 of 3 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Genome sequenceFASTA306.53 MB2018-03-15
Genome sequenceFASTA16.34 KB2018-03-15
Coding SequenceFASTA330.99 MB2018-03-15
Coding SequenceFASTA20.62 KB2018-03-15
Coding SequenceFASTA54.01 KB2018-03-15
protein sequenceFASTA11.18 MB2018-03-15
annotationGFF68.52 KB2018-03-15
annotationGFF1.88 KB2018-03-15
annotationGFF17.76 MB2018-03-15
otherTAR49.71 MB2018-03-15
Displaying 1-10 of 23 File(s).
Funding body Awardee Award ID Comments
Taipei Zoo EY Chuang No 13 2015 Animal Adoption Programs of Taipei Zoo
Date Action
April 5, 2018 Dataset publish
July 9, 2018 Manuscript Link added : 10.1093/gigascience/giy044