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Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives
BACKGROUND: Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729692/ https://www.ncbi.nlm.nih.gov/pubmed/29149296 http://dx.doi.org/10.1093/gigascience/gix105 |
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author | Tang, Qianzi Gu, Yiren Zhou, Xuming Jin, Long Guan, Jiuqiang Liu, Rui Li, Jing Long, Kereng Tian, Shilin Che, Tiandong Hu, Silu Liang, Yan Yang, Xuemei Tao, Xuan Zhong, Zhijun Wang, Guosong Chen, Xiaohui Li, Diyan Ma, Jideng Wang, Xun Mai, Miaomiao Jiang, An’an Luo, Xiaolin Lv, Xuebin Gladyshev, Vadim N Li, Xuewei Li, Mingzhou |
author_facet | Tang, Qianzi Gu, Yiren Zhou, Xuming Jin, Long Guan, Jiuqiang Liu, Rui Li, Jing Long, Kereng Tian, Shilin Che, Tiandong Hu, Silu Liang, Yan Yang, Xuemei Tao, Xuan Zhong, Zhijun Wang, Guosong Chen, Xiaohui Li, Diyan Ma, Jideng Wang, Xun Mai, Miaomiao Jiang, An’an Luo, Xiaolin Lv, Xuebin Gladyshev, Vadim N Li, Xuewei Li, Mingzhou |
author_sort | Tang, Qianzi |
collection | PubMed |
description | BACKGROUND: Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. FINDINGS: We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression–based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation. CONCLUSIONS: These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments. |
format | Online Article Text |
id | pubmed-5729692 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-57296922017-12-18 Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives Tang, Qianzi Gu, Yiren Zhou, Xuming Jin, Long Guan, Jiuqiang Liu, Rui Li, Jing Long, Kereng Tian, Shilin Che, Tiandong Hu, Silu Liang, Yan Yang, Xuemei Tao, Xuan Zhong, Zhijun Wang, Guosong Chen, Xiaohui Li, Diyan Ma, Jideng Wang, Xun Mai, Miaomiao Jiang, An’an Luo, Xiaolin Lv, Xuebin Gladyshev, Vadim N Li, Xuewei Li, Mingzhou Gigascience Data Note BACKGROUND: Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. FINDINGS: We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression–based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation. CONCLUSIONS: These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments. Oxford University Press 2017-11-15 /pmc/articles/PMC5729692/ /pubmed/29149296 http://dx.doi.org/10.1093/gigascience/gix105 Text en © The Authors 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Data Note Tang, Qianzi Gu, Yiren Zhou, Xuming Jin, Long Guan, Jiuqiang Liu, Rui Li, Jing Long, Kereng Tian, Shilin Che, Tiandong Hu, Silu Liang, Yan Yang, Xuemei Tao, Xuan Zhong, Zhijun Wang, Guosong Chen, Xiaohui Li, Diyan Ma, Jideng Wang, Xun Mai, Miaomiao Jiang, An’an Luo, Xiaolin Lv, Xuebin Gladyshev, Vadim N Li, Xuewei Li, Mingzhou Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives |
title | Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives |
title_full | Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives |
title_fullStr | Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives |
title_full_unstemmed | Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives |
title_short | Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives |
title_sort | comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives |
topic | Data Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729692/ https://www.ncbi.nlm.nih.gov/pubmed/29149296 http://dx.doi.org/10.1093/gigascience/gix105 |
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