Whole-Transcriptome Analysis of Yak and Cattle Heart Tissues Reveals Regulatory Pathways Associated With High-Altitude Adaptation

BackgroundThe yak (Bos grunniens) is an important livestock species that can survive the extremely cold, harsh, and oxygen-poor conditions of the Qinghai-Tibetan Plateau and provide meat, milk, and transportation for the Tibetans living there. However, the regulatory network that drive this hypoxic adaptation remain elusive.ResultsThe heart tissues from LeiRoqi (LWQY) yak and their related cattle (Bos Taurus) breeds, which are two native cattle breeds located in high altitude (HAC) and low altitude (LAC) regions, respectively, were collected for RNA sequencing. A total of 178 co-differentially expressed protein-coding transcripts (co-DETs) were discovered in each of the LAC-vs-LWQY and LAC-vs-HAC comparison groups, including NFATC2, NFATC1, ENPP2, ACSL4, BAD, and many other genes whose functions were reported to be associated with the immune-system, endocrine-system, and lipid metabolism. Two and 230 lncRNA transcripts were differentially expressed in the LAC-vs-LWQY and LAC-vs-HAC comparisons’ respectively, but no lncRNA transcripts that were co-differentially expressed. Among the 58 miRNAs that were co-differentially expressed, 18 were up-regulated and 40 were down-regulated. In addition, 640 (501 up-regulated and 139 down-regulated) and 152 (152 up-regulated and one down-regulated) circRNAs showed differential expression in LAC-vs-LWQY and LAC-vs-HAC comparison groups, respectively, and 53 up-regulated co-differentially expressed circRNAs were shared. Multiple co-DETs, which are the targets of miRNAs/lncRNAs, are significantly enriched in high-altitude adaptation related processes, such as, T cell receptor signaling, VEGF signaling, and cAMP signaling. A competing endogenous RNA (ceRNA) network was constructed by integrating the competing relationships among co-differentially expressed mRNAs, miRNAs, lncRNAs and circRNAs. Furthermore, the hypoxic adaptation related ceRNA network was constructed, and the six mRNAs (MAPKAPK3, PXN, NFATC2, ATP7A, DIAPH1, and F2R), the eight miRNAs (including miR-195), and 15 circRNAs (including novel-circ-017096 and novel-circ-018073) are proposed as novel and promising candidates for regulation of hypoxic adaptation in the heart.ConclusionIn conclusion, the data recorded in the present study provides new insights into the molecular network of high-altitude adaptation along with more detailed information of protein-coding transcripts and non-coding transcripts involved in this physiological process, the detailed mechanisms behind how these transcripts “crosstalk” with each other during the plateau adaptation are worthy of future research efforts.

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Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

10.21203/rs.2.10149/v1 ◽

2019 ◽

Author(s):

Hui Wang ◽

Chai Zhixin ◽

Zhong Jincheng ◽

Chen Zhi ◽

Zhu Jiangjiang ◽

...

Keyword(s):

High Altitude ◽

Differentially Expressed ◽

Future Research ◽

Protein Coding ◽

Regulatory Pathways ◽

High Altitude Adaptation ◽

Cerna Network ◽

Hypoxic Adaptation ◽

Comparison Groups ◽

Altitude Adaptation

Abstract Background: the yak (Bos grunniens) is one of the major livestock that can survive the extremely cold, harsh and oxygen-poor conditions and provide meat, milk and transportation for Tibetans living in the Qinghai-Tibetan Plateau, and there are some cattle migrate to yak habitat but cannot survive the extremely conditions well. However, the regulatory mechanisms that drive hypoxic adaptation of yak remain elusive. Results: Thus, we collected heart tissues from Leiwuqi (LWQ) yak and their relatives, the migration cattle in LWQ yak habitat (HAC) and low-altitude cattle (LAC), respectively, for RNA sequencing, 178 co-differentially expressed protein-coding transcripts (CETs) including 6 down-regulated and 172 up-regulated CETs were discovered in both LAC-vs-LWQY and LAC-vs-HAC comparison groups. There were 133, 11 and 3 lncRNA transcripts were specific expressed in LWQY, HAC, and LAC groups, respectively. 2 and 230 lncRNA transcripts differentially expressed in LAC-vs-LWQY and LAC-vs-HAC，respectively, but no lncRNA transcripts co-differentially expressed in those two comparison groups. Among the 58 miRNAs that were co-differentially expressed, 18 were up-regulated and 40 were down-regulated. In addition, 640 (501 up-regulated and 139 down-regulated) and 152 (152 up-regulated and 1 down-regulated) circRNAs showed differential expression in LAC-vs-LWQY and LAC-vs-HAC comparison groups, respectively, and 53 up-regulated co-differentially expressed circRNAs were shared. Multiply CETs which are the target genes for miRNAs/lncRNAs were significantly enriched in high-altitude adaptation related processes, for instance, T cell receptor signaling, VEGF signaling, and cAMP signaling. A competing endogenous RNA (ceRNA) network by integrating competing relationships among CETs, miRNAs, lncRNAs and circRNAs were constructed. Furthermore, we constructed a hypoxic adaptation related ceRNA network to identified that 8 miRNAs and 15 circRNAs were predicted to regulated MAPKAPK3, PXN, NFATC2, ATP7A, DIAPH1 and F2R genes. Conclusion: In conclusion, our data reinforce the view that the molecular network of high-altitude adaptation is composed of several protein-coding transcripts and non-coding transcripts that involved in multiply hypoxic adaptation regulatory pathways. The detailed mechanism for how this network crosstalk each other in heart of Bovidae are worthy of future research efforts.

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Pectoral muscle transcriptome analyses reveal high-altitude adaptations in Tibetan chickens

Animal Biology ◽

10.1163/15707563-bja10026 ◽

2020 ◽

Vol 70 (4) ◽

pp. 385-400

Author(s):

Yaodong Hu ◽

Jiayu Su ◽

Liyuan Cheng ◽

Dan Lan ◽

Diyan Li

Keyword(s):

High Altitude ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Pectoral Muscle ◽

Mapk Signaling ◽

Differentially Expressed ◽

Future Research ◽

Protein Coding ◽

Sequencing Technologies ◽

Tibetan Chicken

Abstract The largest muscles in fowl are the pectorals, which provide the power required for birds to fly. Tibetan chickens show specific adaptations to high-altitude conditions, but changes in the muscle transcriptome associated with these adaptations have not been characterized yet. Therefore, in this study, we used next-generation sequencing technologies to generate eight libraries of mRNA sequences for four Tibetan chickens and four Beijing fatty chickens. A comprehensive transcriptome analysis was performed. In the eight samples, 12 333 annotated protein-coding genes were expressed. Among these, 48 differentially expressed genes were found; all of which were upregulated in Tibetan chickens. These differentially expressed genes were mainly involved in kidney morphogenesis, which indicates that hypoxia has an important effect on renal tubule development. Only nine genes were involved in Kyoto Encyclopedia of Genes and Genomes pathways, such as the endocytosis pathway, the MAPK signaling pathway, the calcium signaling pathway and the TGF-beta signaling pathway. The differentially expressed genes identified in this study will be used to facilitate future research into the Tibetan chicken.

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High-altitude adaptation and incipient speciation in geladas

10.1101/2021.09.01.458582 ◽

2021 ◽

Author(s):

Kenneth L Chiou ◽

Mareike C Janiak ◽

India Schneider-Crease ◽

Sharmi Sen ◽

Ferehiwot Ayele ◽

...

Keyword(s):

High Altitude ◽

Gene Families ◽

Extreme Conditions ◽

Morphometric Data ◽

Incipient Speciation ◽

Protein Coding ◽

Coding Sequences ◽

High Altitude Adaptation ◽

Altitude Adaptation ◽

Insight Into

Survival at high altitude requires adapting to extreme conditions such as environmental hypoxia. To understand high-altitude adaptations in a primate, we assembled the genome of the gelada (Theropithecus gelada), an endemic Ethiopian monkey, and complemented it with population resequencing, hematological, and morphometric data. Unexpectedly, we identified a novel karyotype that may contribute to reproductive isolation between gelada populations. We also identified genomic elements including protein-coding sequences and gene families that exhibit accelerated changes in geladas and may contribute to high-altitude adaptation. Our findings lend insight into mechanisms of speciation and adaptation while providing promising avenues for functional hypoxia research.

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Faculty Opinions recommendation of The molecular basis of high-altitude adaptation in deer mice.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1079774.532691 ◽

2007 ◽

Author(s):

Ary Hoffmann

Keyword(s):

High Altitude ◽

Molecular Basis ◽

Deer Mice ◽

High Altitude Adaptation ◽

Altitude Adaptation

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Faculty Opinions recommendation of Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1163704.625482 ◽

2009 ◽

Author(s):

Anthony Zera

Keyword(s):

High Altitude ◽

Deer Mouse ◽

High Altitude Adaptation ◽

Altitude Adaptation

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Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

Genome Biology and Evolution ◽

10.1093/gbe/evab014 ◽

2021 ◽

Author(s):

Pamela Wiener ◽

Christelle Robert ◽

Abulgasim Ahbara ◽

Mazdak Salavati ◽

Ayele Abebe ◽

...

Keyword(s):

High Altitude ◽

Environmental Variables ◽

Large Scale ◽

Sequence Data ◽

Strong Association ◽

Environmental Adaptation ◽

Whole Genome Sequence ◽

Single Nucleotide Variants ◽

High Altitude Adaptation ◽

Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

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