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Detection and Integrated Analysis of LncRNA and mRNA Relevant to Plateau Adaptation of Yak

ABSTRACT: Detection and Integrated Analysis of LncRNA and mRNA Relevant to Plateau Adaptation of Yak

PROVIDER: PRJNA548123 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9259120_1.fastq.gz	Fastqsanger.gz
	SRR9259120_2.fastq.gz	Fastqsanger.gz
	SRR9259130_1.fastq.gz	Fastqsanger.gz
	SRR9259130_2.fastq.gz	Fastqsanger.gz
	SRR9259121_1.fastq.gz	Fastqsanger.gz

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Detection and Integrated Analysis of LncRNA and mRNA Relevant to Plateau Adaptation of Yak

Project description:Analysis of RNA-seq of cerebellum and cerebrum in Yak, Yakow and Cattle.The result reveal the relationship between modules and Plateau Adaptation trait

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Detection and integrated analysis of lncRNA and mRNA relevant to plateau adaptation of Yak.

Project description:Known as the 'ship of the plateau', through thousands of years evolution and cruelty environments selection containing low oxygen and strong ultraviolet radiation, yaks have adapted plateau environments and supplied important goods and materials for the people in the Qinghai-Tibet Plateau. This study aimed to identify differentially expressed (DE) genes and novel long non-coding RNAs (lncRNAs) of yaks for the Plateau adaptation and their underlying co-expression and regulatory network. We carried out RNA-seq analysis for cerebral and cerebellar tissue specimens of Bos taurus, Bos grunniens × Bos Taurus and B. grunniens. Furthermore, 12,072 pseudo lncRNAs were predicted using three software. In total, 4,257 significant DE transcripts were identified using the Ballgown R package (p < .01), of which 1,021 were protein-coding genes, 14 were known lncRNAs, and 661 were novel lncRNAs. Using WGCNA, a co-expression network of DE mRNAs and lncRNAs comprising 5 modules was generated to determine functional associations clusters. This study reveals a valuable sub-network comprising 8 hub genes, one known lncRNA and 5 novel lncRNAs in the major module. These hub genes are associated with blood pressure regulation, generation of reactive oxygen species and metabolism. The analysis of co-expressed genes thus provides a basis for the regulatory mechanisms in PA in Yaks and for the detection of additional genes between cross-breed and parent populations.

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Exploring the mechanisms of high-altitude adaptation in yak based on single-cell transcriptome atlas.

Project description:This study explores how yaks, an ideal animal model for studying plateau adaptability, adapt to high-altitude environments. The lung is a representative organ of the yak’s adaptation to high-altitude environments. The F1 hybrids of yak and cattle, known as dzho, also exhibit adaptability to plateau conditions. This study constructed a single-cell transcriptome atlas of the lungs in yak, dzho and cattle, containing 51 subtypes. We initially found that the differential subtypes among yak, dzho and cattle were mainly concentrated in T&NK cells and fibroblasts. Most of them belonged to new cell subtypes. Subsequently, we speculated that NKG7 and CD4 played a central regulatory role in T&NK cells, contributing to T cell activation and affecting the adaptive immune response of yaks. In fibroblasts, MYL9 and IGF2 are believed to play key regulatory roles, participating in maintaining cellular energy metabolism balance. These results provide an important scientific basis for systematically analysing the molecular regulatory mechanisms of yak adaptation to high-altitude hypoxia.

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Molecular mechanisms in lung tissue of yak provide insights into high-altitude adaptation by transcriptome-wide analysis [RNA-seq]

Project description:Purpose：Yak long-term colonization and widespread distribution across the plateau can be serve as an ideal natural animal model to provide insights into the adaptive evolution of other plateau species, including humans. Methods:To exploring the molecular mechanisms of lung tissue in yak to response to hypoxia, the mRNA, lncRNA and miRNA of lung tissue from cattle and three different altitude yaks were sequenced. Results:A total of 21764 mRNAs, 14168 lncRNAs and 1209miRNAs (305 known and 904 novel miRNAs)were identifed.Compared yak with cattle, 4975 mRNAs, 3326 lncRNAs and 75 miRNAs were differentially expressed. 756 mRNAs, 346 lncRNAs and 83 miRNAs were found to be differentially expressed amongthree different altitude yaks(fold change≥2 and P-value<0.05). Conclusions:The differentially expressed genes were functionally enriched in long-chain fatty acid metabolic process and protein processing between yak and cattle, while the immune response and cell cycle were enriched among three different altitude yaks. Furthermore, the competing endogenous RNAs (ceRNAs) networks were identified to illustrate their roles.

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Molecular mechanisms in lung tissue of yak provide insights into high-altitude adaptation by transcriptome-wide analysis [miRNA-seq]

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Feces sample of plateau pika and yak

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Comprehensive analysis of differentially expressed mRNA, circRNA and miRNA and their ceRNA networks in testis of cattle-yak, yak and cattle

Project description:Cattle-yak is the hybrid offspring of yak and cattle. It has obvious heterosis in production performance, but the male sterility of cattle-yak has always been the focus of attention. Studies have shown that non-coding RNA is involved in the regulation of spermatogenesis. We comprehensively compared the testicular transcription profiles of cattle, yak and cattle-yak. More DEGs, DECs and DEMs were found in the intersection of the two comparison groups of cattle and cattle-yak, yak and cattle-yak, with 4,968, 360 and 59, respectively. The DEGs of cattle-yak, cattle and yak were mainly enriched in biological processes such as spermatogenesis, male gamete generation and sexual reproduction. At the same time, GO and KEGG analysis suggested that DECs host genes and DEMs source genes were also involved in the regulation of spermatogenesis. The construction of potential ceRNA networks found that some differentially expressed ncRNAs may be involved in the regulation of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, miR-15b, etc., as well as unreported miR-6123, miR-1306 and some miRNA and circRNA interaction pairs. This study provides a reference for further study on the mechanism of male sterility in cattle-yak.

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