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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

Additional files

Additional file 1:

Tables S1-S13 and Figures S1-S7. Table S1. Summary of the sequencing data of P. humilis. Table S2. Statistics of ground tit genome assembly. Table S3. Statistics of transposable elements detected in the ground tit assembly. Table S4. Comparison of transposable elements among chicken, zebra finch, and ground tit. Table S5. General statistics of each gene set and integrated predictions. Table S6. Genes annotated via functional databases. Table S7. Statistics of ncRNA prediction in the assembly. Tables S8-S10. Functional analysis of gene families of expansion and contraction in ground tit. Tables S11-S13. Analysis of rapidly and slowly evolving categories. Figure S1. Local GC content distribution of the P. humilis, chicken, zebra finch, and human genomes. Figure S2. Comparison of gene parameters between ground tit and chicken, zebra finch, and human. Figure S3. Supporting evidence for gene models. Figure S4. Distribution of orthologous protein identities between chicken and other species for a subset of strictly conserved single-copy orthologs. Figure S5. Micro-synteny between genomes of chicken and ground tit. Figure S6. Venn diagram showing the amount of sequence (in Mbp) aligned among the three avian genomes. Figure S7. Dynamic evolution of orthologous gene clusters.

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