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ABSTRACT:
PROVIDER: PRJNA682510 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: High-altitude adaptive evolution of transcription, and the convergence and divergence of transcriptional alteration across species in response to high-altitude environments, is an important topic of broad interest to the general biology community. Our study aims to answer this important biological question. Methods: We generated deep transcriptome data of high- and low- altitude populations across four species: chicken, pig, goat and sheep, as well as high-altitude yak and low-altitude cattle, from six tissues (heart, kidney, liver, lung, skeletal muscle and spleen). Results: Here we provide a comprehensive comparative transcriptome landscape of expression and alternative splicing variation between low- and high-altitude populations across multiple species for distinct tissues. Conclusions: Our data serves a valuable resource for further study on adaptive transcription evolution and identification of candidate adaptive genes.
2017-09-06 | GSE93855 | GEO
Project description:The first gut metagenome of wild Bar-headed geese
| PRJEB12153 | ENA
Project description:Extreme environmental conditions at high altitude, such as hypobaric hypoxia, low temperature, and strong UV radiation, pose a great challenge to the survival of animals. Although the mechanisms of adaptation to high-altitude environments have attracted much attention for native plateau species, the underlying metabolic regulation remains unclear. Here, we used a multi-platform metabolomic analysis to compare metabolic profiles of liver between high- and low-altitude populations of toad-headed lizards, Phrynocephalus vlangalii, from the Qinghai-Tibet Plateau. A total of 191 differential metabolites were identified, consisting of 108 up-regulated and 83 down-regulated metabolites in high-altitude lizards as compared with values for low-altitude lizards. Pathway analysis revealed that the significantly different metabolites were associated with carbohydrate metabolism, amino acid metabolism, purine metabolism, and glycerolipid metabolism. Most intermediary metabolites of glycolysis and the tricarboxylic acid cycle were not significantly altered between the two altitudes, but most free fatty acids as well as β-hydroxybutyric acid were significantly lower in the high-altitude population. This may suggest that high-altitude lizards rely more on carbohydrates as their main energy fuel rather than lipids. Higher levels of phospholipids occurred in the liver of high-altitude populations, suggesting that membrane lipids may undergo adaptive remodeling in response to low-temperature stress at high altitude. In summary, this study demonstrates that metabolic profiles differ substantially between high- and low-altitude lizard populations, and that these differential metabolites and metabolic pathways can provide new insights to reveal mechanisms of adaptation to extreme environments at high altitude.
2024-01-16 | MTBLS6900 | MetaboLights
Project description:To explore the exceptional mechanisms of gene expression and DNA methylation that are induced by low altitude environments in Tibetan pigs, we performed a comparative transcriptomic analysis of skeletal muscle in indigenous Tibetan pigs that reside in high altitude regions (～4,000 m) and their counterparts that migrated to the geographically neighboring low-altitude regions (～500 m) for nearly ten generations. We identified protein coding genes that related to hypoxia response (EGLN3 and FLT1), oxygen transport and energy metabolism (TFB2M), and two long non-coding RNAs (TCONS_00039686 and TCONS_00084992) that associated with the regulation of transcription and various nucleolus and organelle lumen, were differentially expressed between Tibetan pigs and their counterparts in low-altitude regions, thus might be the potential candidate regulators in skeletal muscle of low-altitude acclimation in Tibetan pigs. We also found genes embedded in differentially methylated regions between Tibetan pigs and their counterparts in low-altitude regions were mainly involved in ‘Starch and sucrose metabolism’, ‘glucuronosyltransferase activity’ processes, hypoxia and energy metabolism. We envision that this study will serve as a valuable resource for mammal acclimatization research and agricultural food industry.
2017-11-25 | GSE90511 | GEO
Project description:To explore the exceptional mechanisms of gene expression and DNA methylation that are induced by low altitude environments in Tibetan pigs, we performed a comparative transcriptomic analysis of skeletal muscle in indigenous Tibetan pigs that reside in high altitude regions (～4,000 m) and their counterparts that migrated to the geographically neighboring low-altitude regions (～500 m) for nearly ten generations. We identified protein coding genes that related to hypoxia response (EGLN3 and FLT1), oxygen transport and energy metabolism (TFB2M), and two long non-coding RNAs (TCONS_00039686 and TCONS_00084992) that associated with the regulation of transcription and various nucleolus and organelle lumen, were differentially expressed between Tibetan pigs and their counterparts in low-altitude regions, thus might be the potential candidate regulators in skeletal muscle of low-altitude acclimation in Tibetan pigs. We also found genes embedded in differentially methylated regions between Tibetan pigs and their counterparts in low-altitude regions were mainly involved in ‘Starch and sucrose metabolism’, ‘glucuronosyltransferase activity’ processes, hypoxia and energy metabolism. We envision that this study will serve as a valuable resource for mammal acclimatization research and agricultural food industry.
2017-11-25 | GSE90510 | GEO
Project description:Lion-head goose is the only large goose species in China, and it was one of the largest goose species in the world. Our previous study firstly reported a chromosome-level genome assembly of Lion-head goose (Anser cygnoides), a native breed in South China, through the combination of PacBio, Bionano, and Hi-C technologies. The fat content of foie gras is augmented during its preparation due to the special feeding regimen. Lion-head geese have a strong tolerance of massive energy intake and show a priority of fat accumulation in liver tissue. In this study, we studied for the first time the important differential genes that regulate fatty liver in Lion-head goose. After high-intake feeding, the fatty livers of Lion-head geese were distinctly characterized. The revelation of gene regulation is an important basis for the study of liver development and molecular characteristics for the Lion-head goose. To analyze the excellent fatty liver performance of Lion-head goose at the molecular level, we performed whole transcriptome analysis by high-throughput RNA sequencing to analyze the key regulatory genes that determine the fatty livers in high-intake feeding group compared with the normal livers in normally-fed Lion-head geese. We identified 716 differentially expressed mRNAs, 145 differentially expressed circRNAs, and 39 differentially expressed lncRNAs in the fatty livers in high-intake feeding group compared with the normal livers in normally-fed Lion-head geese, including upregulated and downregulated genes, respectively. GO enrichment analysis showed that these genes were significantly enriched in molecular function, involved in extracellular regions, DNA-binding transcription factor activity, extracellular matrix, heme binding and other life activities. We chose differentially expressed genes involved in either upregulation or downregulation, and we additionally confirmed the accuracy of sequencing at the RNA level. In summary, our research suggested that these differentially expressed genes may play important roles in fatty liver development in Lion-head goose. However, the functions and mechanisms of these significantly differentially expressed genes should be investigated in future studies.
2023-11-16 | GSE243829 | GEO