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

Genome Biology

Jun Wang¹  Yingrui Li²  Longhai Luo²  Jinchao Liu²  Rongjun He²  Xinming Zhang²  Zhaobao Wang²  Songbo Wang²  Jinyang Zhao²  Meirong Hao²  Yue Cai²  Caiyun Gou²  Yuanyuan Hui²  Shengkai Pan²  Jiaohui Xu²  Yadan Luo²  Yongshan Lang²  Xiaoju Qian²  Qingle Cai² 

[1] King Abdulaziz University, Abdulla Alsulaiman Road, Jeddah 21589, Saudi Arabia;BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China

关键词: phylogeny;    high-altitude adaptation;    genome;   

Others  :  866869
DOI  :  10.1186/gb-2013-14-3-r29

 received in 2012-07-23, accepted in 2013-03-28,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Cai et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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