The yak genome and adaptation to life at high altitude

Qiu, Qiang; Zhang, Guojie; Ma, Tao; Qian, Wubin; Wang, Junyi; Ye, Zhiqiang; Cao, C; Hu, Quanjun; Kim, Jaebum; Larkin, Denis M.; Auvil, Loretta; Capitanu, Boris; Ma, Jian; Lewin, Harris A.; Qian, Xiaoju; Lang, Yongshan; Zhou, Ran; Wang, Lizhong; Wang, Kun; Xia, Jinquan; Liao, Sheng-Guang; Pan, Shengkai; Lu, Xu; Hou, Haolong; Wang, Yan; Zang, Xuetao; Yin, Ye; Ma, Hongyu; Zhang, Jian; Wang, Zhaofeng; Zhang, Yingmei; Zhang, Dawei; Yonezawa, Takahiro; Hasegawa, Masami; Zhong, Yang; Liu, Wenbin; Zhang, Yan; Huang, Zhiyong; Zhang, Shengxiang; Long, Ruijun; Yang, Huanming; Wang, Jian; Lenstra, Johannes A.; Cooper, David Neil; Wu, Yi; Wang, Jun; Shi, Peng; Liu, Jianquan

doi:10.1038/ng.2343

Cited by 769 publications

(767 citation statements)

References 66 publications

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“…5b). relatives (Qiu et al 2012;Cai et al 2013). With regard to ADAM9, previous study has showed that the mRNA and protein expression levels of this gene are elevated by the 14 regulation of reactive oxygen species under hypoxic stress conditions in prostate cancer cells (Shen et al 2013).…”

Section: Signatures Of Deleterious Variation and Positive Selectionmentioning

confidence: 99%

Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys

et al. 2016

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Snub-nosed monkeys (genus Rhinopithecus) are a group of endangered colobines 2 endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population 4 genomic analyses, we observed an similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic 6 diversity was lower than that reported in other primates. Reconstruction of Rhinopithecus evolutionary history suggested that episodes of climatic variation over 8 the past 2 million years, associated with glacial advances and retreats and population isolation, have shaped snub-nosed monkey demography and evolution. We further 10 identified several hypoxia-related genes under selection in R. bieti (black snub-nosed monkey), a species that exploits habitats higher than any other nonhuman primate. 12These results provide the first detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden and adaptation in this radiation of 14 endangered primates. 16

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Section: Signatures Of Deleterious Variation and Positive Selectionmentioning

confidence: 99%

Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys

et al. 2016

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“…Positively selected and rapidly evolving genes in the yak lineage are also found to be significantly enriched in functional categories and pathways related to hypoxia and nutrition metabolism. These findings may have important implications for understanding adaptation to higher altitudes in other animal species and for hypoxia-related diseases in humans (Qiu et al, 2012).…”

Section: Introductionmentioning

confidence: 84%

Profiling of the yak skeletal muscle tissue gene expression and comparison with the domestic cattle by genome array

Wang

Liu

Zhang

2014

Animal

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Of all the mammals of the world, the yak lives at the highest altitude area of more than 3000 m. Comparison between yak and cattle of the low-altitude areas will be informative in studying animal adaptation to higher altitudes. To investigate the molecular mechanism involved in meat quality differences between the two Chinese special varieties Qinghai yak and Qinchuan cattle, 12 chemical-physical characteristics of the longissimus dorsi muscle related to meat quality were compared at the age of 36 months, and the gene expression profiles were constructed by utilizing the bovine genome array. Significant analysis of microarrays was used to identify the differentially expressed genes. Gene ontology and pathway analysis were performed by a free Web-based Molecular Annotation System 2.0. The results reveal~11 000 probes representing about 10 000 genes that were detected in both the Qinghai yak and Qinchuan cattle. A total of 1922 genes were shown to be differentially expressed, 633 probes were upregulated and 1259 probes were downregulated in the muscle tissue of Qinghai yak that were mainly involved in ubiquitin-mediated proteolysis, muscle growth regulation, glucose metabolism, immune response and so on. Quantitative real-time PCR (qRT-PCR) was performed to validate some differentially expressed genes identified by microarray. Further analysis implied that animals living at a high altitude may supply energy by more active protein catabolism and glycolysis compared with those living in the plain areas. Our results establish the groundwork for further studies on yaks' meat quality and will be beneficial in improving the yaks' breeding by molecular biotechnology.

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“…Using either experimentally determined gene/protein function or sequence similarity to previously identified functions, the activities of individual genes are paired with specific numeric codes. Gene Ontology analyses have been used in other studies to determine the functional components to a variety of traits, adaptations and physiologies of interest, including adaptation to high altitudes (Qiu et al, 2012), depth tolerance in deep-sea bacteria (Vezzi et al, 2005), and a number of human disorders (Ahn et al, 2003;Holmans et al, 2009); however, these have identified known genes of interest and then drawn conclusions of function popt hoc. Rather than assigning the Gene Ontology codes first and subsequently determining the functions of particular interest as has been done previously, we can select functions of expected relevance a priori in order to allow for quantitative testing of their adaptive relevance by comparing functions in genomes in species that exhibit a convergent function.…”

Section: Intnoductionmentioning

confidence: 99%

Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics

Wheeler

Carstens

2018

Preprint

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Carnivorous plants are striking examples of evolutionary convergence, displaying complex and often highly similar adaptations despite lack of shared ancestry. Using available carnivorous plant genomes along with non-carnivorous reference taxa, this study examines the convergence of functional overrepresentation of genes previously implicated in plant carnivory. Gene Ontology (GO) coding was used to quantitatively score functional representation in these taxa, in terms of proportion of carnivory-associated functions relative to all functional sequence. Statistical analysis revealed that, in carnivorous plants as a group, only two of the 24 functions tested showed a signal of substantial overrepresentation. However, when the four carnivorous taxa were analyzed individually, 11 functions were found to be significant in at least one taxon. Though carnivorous plants collectively may show overrepresentation in functions from the predicted set, the specific functions that are overrepresented vary substantially from taxon to taxon. While it is possible that some functions serve a similar practical purpose such that one taxon does not need to utilize both to achieve the same result, it appears that there are multiple approaches for the evolution of carnivorous function in plant genomes. Our approach could be applied to tests of functional convergence in other systems provided on the availability of genomes and annotation data for a group.

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The yak genome and adaptation to life at high altitude

Cited by 769 publications

References 66 publications

Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys

Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys

Profiling of the yak skeletal muscle tissue gene expression and comparison with the domestic cattle by genome array

Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics

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