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

Qingle Cai1, Xiaoju Qian1, Yongshan Lang1, Yadan Luo1, Jiaohui Xu1, Shengkai Pan1, Yuanyuan Hui1, Caiyun Gou1, Yue Cai1, Meirong Hao1, Jinyang Zhao1, Songbo Wang1, Zhaobao Wang1, Xinming Zhang1, Rongjun He1, Jinchao Liu1, Longhai Luo1, Yingrui Li1 and Jun Wang123*

Author Affiliations

1 BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China

2 Department of Biology, University of Copenhagen, DK-1165 Copenhagen, Denmark

3 King Abdulaziz University, Abdulla Alsulaiman Road, Jeddah 21589, Saudi Arabia

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Genome Biology 2013, 14:R29  doi:10.1186/gb-2013-14-3-r29

Published: 28 March 2013

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.

Keywords:
genome; high-altitude adaptation; phylogeny