Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude.
Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude.
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DOI：
10.1186/gb-2013-14-3-r29
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发表时间：
2013-03-28
期刊：
影响因子：
12.3
通讯作者：
Wang J
中科院分区：
文献类型：
--
作者：
Cai Q;Qian X;Lang Y;Luo Y;Xu J;Pan S;Hui Y;Gou C;Cai Y;Hao M;Zhao J;Wang S;Wang Z;Zhang X;He R;Liu J;Luo L;Li Y;Wang J
对某些哺乳动物的高海拔适应机制进行了研究。然而，在鸟类物种，如地山雀Pseudopodoces humilis，适应机制仍然不清楚。地山雀的生殖也是有争议的。利用下一代测序技术，我们生成并组装了地山雀的基因组序列草图。该组装体包含1.04 Gb的序列，覆盖整个基因组的95.4%，并且在支架和重叠群水平上具有比其他测序的禽类基因组更高的N50值。检测到约170万个SNP，预测了16，998个蛋白质编码基因，并确定了7%的基因组为重复序列。地山雀基因组与其他鸟类基因组的比较揭示了一个保守的基因组结构，并证实了地山雀不属于鸦科。基因家族扩展和正选择基因分析揭示了与心脏功能相关的基因。我们的研究结果有助于我们了解该物种对极端环境生活条件的适应。我们的数据和分析有助于研究鸟类的进化历史，并为动物对极端条件的适应机制提供新的见解。
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. 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. 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.
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影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
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影响因子：
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作者：
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DOI：
10.1073/pnas.1002443107
发表时间：
2010-06-22
影响因子：
11.1
作者：
Beall, Cynthia M.;Cavalleri, Gianpiero L.;Zheng, Yong Tang
通讯作者：
Zheng, Yong Tang