Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude

Cai, Qingle, Qian, Xiaoju, Lang, Yongshan, Luo, Yadan, Xu, Jiaohui, Pan, Shengkai, Hui, Yuanyuan, Gou, Caiyun, Cai, Yue, Hao, Meirong, Zhao, Jinyang, Wang, Songbo, Wang, Zhaobao, Zhang, Xinming, He, Rongjun, Liu, Jinchao, Luo, Longhai, Li, Yingrui and Wang, Jun (2013) Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude. Genome Biology, 14 3: R29-R29. doi:10.1186/gb-2013-14-3-r29


Author Cai, Qingle
Qian, Xiaoju
Lang, Yongshan
Luo, Yadan
Xu, Jiaohui
Pan, Shengkai
Hui, Yuanyuan
Gou, Caiyun
Cai, Yue
Hao, Meirong
Zhao, Jinyang
Wang, Songbo
Wang, Zhaobao
Zhang, Xinming
He, Rongjun
Liu, Jinchao
Luo, Longhai
Li, Yingrui
Wang, Jun
Title Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude
Journal name Genome Biology   Check publisher's open access policy
ISSN 1474-760X
Publication date 2013-03-28
Sub-type Article (original research)
DOI 10.1186/gb-2013-14-3-r29
Open Access Status DOI
Volume 14
Issue 3
Start page R29
End page R29
Total pages 12
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Abstract Background: The mechanism of high-altitude adaptation has been studied in certain mammals. However, in avian species like the ground tit Pseudopodoces humilis, the adaptation mechanism remains unclear. The phylogeny of the ground tit is also controversial.Results: Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit. The assembly contained 1.04 Gb of sequence that covered 95.4% of the whole genome and had higher N50 values, at the level of both scaffolds and contigs, than other sequenced avian genomes. About 1.7 million SNPs were detected, 16,998 protein-coding genes were predicted and 7% of the genome was identified as repeat sequences. Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family. Gene family expansion and positively selected gene analysis revealed genes that were related to cardiac function. Our findings contribute to our understanding of the adaptation of this species to extreme environmental living conditions.Conclusions: Our data and analysis contribute to the study of avian evolutionary history and provide new insights into the adaptation mechanisms to extreme conditions in animals.
Keyword Genome
High altitude adaptation
Phylogeny
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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