Supporting data for "Comparative transcriptomics of five high-altitude vertebrates and their low-altitude relatives"

Dataset type: Transcriptomic
Data released on October 23, 2017

Tang Q; Gu Y; Zhou X; Jin L; Guan J; Liu R; Li J; Long K; Tian S; Che T; Hu S; Liang Y; Yang X; Tao X; Zhong Z; Wang G; Chen X; Li D; Ma J; Wang X; Mai M; Jiang A; Luo X; Lv X; Gladyshev VN; Li X; Li M (2017): Supporting data for "Comparative transcriptomics of five high-altitude vertebrates and their low-altitude relatives" GigaScience Database. http://dx.doi.org/10.5524/100355

DOI10.5524/100355

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 examined high-altitude adaptation 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.
We generated a total of 910 Gb high-quality RNA-seq data for 180 samples derived from six tissues of five 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 ~70% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.1. 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 were potentially involved in phenotypic divergence shaped by high-altitude adaptation.
This data serves 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.

Additional details

Read the peer-reviewed publication(s):

Tang, Q., Gu, Y., Zhou, X., Jin, L., Guan, J., Liu, R., … Li, M. (2017). Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives. GigaScience, 6(12). doi:10.1093/gigascience/gix105

Accessions (data included in GigaDB):

BioProject: PRJNA357880
BioProject: PRJNA362606





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
H-chicken_heart19031ChickenGallus gallus Description:RNA extracted from heart of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242742
...
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H-chicken_heart29031ChickenGallus gallus Description:RNA extracted from heart of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242739
...
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H-chicken_heart39031ChickenGallus gallus Description:RNA extracted from heart of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242736
...
+
H-chicken_kidney19031ChickenGallus gallus Description:RNA extracted from kidney of an adult ...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242620
...
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H-chicken_kidney29031ChickenGallus gallus Description:RNA extracted from kidney of an adult ...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242619
...
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H-chicken_kidney39031ChickenGallus gallus Description:RNA extracted from kidney of an adult ...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242618
...
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H-chicken_liver19031ChickenGallus gallus Description:RNA extracted from liver of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242707
...
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H-chicken_liver29031ChickenGallus gallus Description:RNA extracted from liver of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242705
...
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H-chicken_liver39031ChickenGallus gallus Description:RNA extracted from liver of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242703
...
+
H-chicken_lung19031ChickenGallus gallus Description:RNA extracted from lung of an adult ch...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242741
...
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Displaying 1-10 of 187 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
ScriptPython3.3 KB2017-09-27
ScriptPython3.84 KB2017-09-27
L-cow_heart1 +Expression dataUNKNOWN264.67 KB2017-09-27
L-cow_kidney1 +Expression dataUNKNOWN292.62 KB2017-09-27
L-cow_liver1 +Expression dataUNKNOWN145.95 KB2017-09-27
L-cow_lung1 +Expression dataUNKNOWN506.17 KB2017-09-27
L-cow_muscle1 +Expression dataUNKNOWN394.61 KB2017-09-27
L-cow_spleen1 +Expression dataUNKNOWN371.45 KB2017-09-27
L-chicken_heart1 +Expression dataUNKNOWN217.65 KB2017-09-27
L-chicken_kidney1 +Expression dataUNKNOWN125.56 KB2017-09-27
Displaying 1-10 of 238 File(s).
Funding body Awardee Award ID Comments
Ministry of Science & Technology of the People's Republic of China M Li 2013AA102502 National High Technology Research and Development Program of China (863 Program)
National Natural Science Foundation of China Q Tang 31402046
National Natural Science Foundation of China M Li 31522055
National Natural Science Foundation of China J Ma 31601918
National Natural Science Foundation of China X Li 31530073
National Natural Science Foundation of China M Li 31472081
Sichuan Provincial Department of Science and Technology Y Gu 2016NYZ0042 Science & Technology Support Program of Sichuan
Sichuan Provincial Department of Science and Technology Y Gu 2017JQ0011 Youth Science Fund of Sichuan
China Postdoctoral Science Foundation Q Tang 2015M572486
China Agriculture Research System Y Gu CARS-36
Sichuan Provincial Department of Science and Technology M Li 2015TD0012 Program for Innovative Research Team of Sichuan Province
Sichuan Provincial Department of Science and Technology Y Gu SCCXTD-005 Program for Pig Industry Technology System Innovation Team of Sichuan Province
Sichuan Provincial Department of Science and Technology X Wang 15ZA0008 Project of Sichuan Education Department
Sichuan Provincial Department of Science and Technology M Li 15ZA0003 Project of Sichuan Education Department
Sichuan Provincial Department of Science and Technology J Ma 16ZA0025 Project of Sichuan Education Department
Sichuan Provincial Department of Science and Technology A Jiang 16ZB0037 Project of Sichuan Education Department
Date Action
October 23, 2017 Dataset publish
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix105