Journal
GIGASCIENCE
Volume 6, Issue 12, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/gix105
Keywords
high-altitude vertebrates; comparative transcriptomics; gene expression; alternative splicing
Categories
Funding
- National High Technology Research and Development Program of China (863 Program) [2013AA102502]
- National Natural Science Foundation of China [31402046, 31522055, 31601918, 31530073, 31472081, 31772576]
- Science and Technology Support Program of Sichuan [2016NYZ0042]
- Youth Science Fund of Sichuan [2017JQ0011]
- China Postdoctoral Science Foundation [2015M572486]
- China Agriculture Research System [CARS36]
- Program for Innovative Research Team of Sichuan Province [2015TD0012]
- Program for Pig Industry Technology System Innovation Team of Sichuan Province [SCCXTD-005]
- Project of Sichuan Education Department [15ZA0008, 15ZA0003, 16ZA0025, 16ZB0037]
- National Program for Support of Top-notch Young Professionals, and the Young Scholars of the Yangtze River
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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, similar to 75% reads could be aligned to their respective reference genomes, and on average similar to 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.
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