The Transcriptome Analysis Of Cerebrum And Cerebellum Reveals The Well Hypoxic Adaptability Of Yak

As an important genetic resource of the Qinghai-Tibet Plateau,yak is important to local animal husbandry economy.To adapt the harsh environment of plateau,yak has evolved some anatomical and physiological characteristics.As brain is the most oxygenconsuming tissue in animal,it is important to explore and excavate the role of brain tissue in yak hypoxic adaptation.In this study,transcriptome sequencing and bioinformatics analysis were performed on the cerebrum and cerebellum tissues of Leiwuqi yak,Tibetan cattle and Sanjiang cattle,respectively,to obtain the differential expression genes between cerebrum and cerebellum tissues,and screen candidate genes related to hypoxic adaptation.Then,RT-qPCR was performed to validate the expression profile of differential expression genes in cerebrum and cerebellum tissues.The results are as follows:Totally,reads ranged from 11,893 Mbp to 16,422 Mbp were obtained among 18 samples with the GC content was about 50%.The percentage of Q30 ranged from 94.75% to 96.32%,and reference genome comparison ratio was ranged from 90.88% to 93.81%.In Leiwuqi yak cerebrum tissues,33,282 mRNA transcripts were obtained,including 12,499 new transcripts and 20,783 known transcripts,and 2,969 lncRNAs were screened,including 2,703 new lncRNAs and 266 known lncRNAs.In yak cerebellum tissues,33,552 mRNAs including 12,544 new transcripts and 21,008 known transcripts were screened,and 3,027 lncRNAs including 2,750 new lncRNAs and 277 known lncRNAs were obtained.In Tibetan cattle cerebrum tissues,we screened 57,158 mRNAs including 11,362 new mRNAs and 45,796 known mRNAs,and 5,404 lncRNAs including 2,014 new lncRNAs and 3,390 known lncRNAs were obtained.In Tibetan cattle cerebellum tissues,56,600 mRNAs(including 11,281 new mRNAs and 45,319 known mRNAs)and 5,295 lncRNAs(including 2,015 new lncRNAs and 3,280 known lncRNAs)were obtained,respectively.In Sanjiang cattle cerebrum tissues,56,477 mRNAs(including 11,208 new mRNAs and 45,269 known mRNAs)and 5,457 lncRNAs(including 2,064 new lncRNAs and 3,393 known lncRNAs)were screened,respectively.In Sanjiang cattle cerebellum tissues,55,389 mRNAs including 10,886 new mRNAs and 44,503 known mRNAs were screened,and 4,830 lncRNAs including 1,781 new lncRNAs and 3,049 known lncRNAs were obtained,respectively.In cerebrum and cerebellum of Leiwuqi yak,2,912 new lncRNAs and 13,162 new mRNAs were screened,and 2,439 new lncRNAs and 13,585 new mRNAs were obtained in cattle,respectively.According to principal component analysis,the first principal component of Leiwuqi yak RNA and lncRNA can distinguish the cerebrum and cerebellum tissues,and the second principal component can distinguish different individuals of yak.The first principal component of RNA and lncRNA of Sanjiang cattle and Tibetan cattle can distinguish the cerebrum and cerebellum tissues,but the second principal component failed to completely differentiate Tibetan cattle and Sanjiang cattle,indicating that the difference between tissues was higher than that between populations.In addition,the expression levels of lncRNA and RNA in different tissues were different.There were 50 lncRNAs and 424 mRNAs differentially expressed between the cerebrum and cerebellum tissue of Leiwuqi yak,respectively.In Sanjiang cattle,329 differential lncRNAs and 2,326 differential mRNA were obtained between the cerebrum and cerebellum tissues,respectively.In addition,in the cerebrum and cerebellum tissue of Tibetan cattle,we obtained 2 lncRNAs and 89 mRNAs differentially expressed.The number of differentially expressed genes was the lowest in Tibetan cattle,followed by the difference between Leiwuqi yak tissues.42 lncRNAs and 374 mRNAs were codifferentially expressed in the cerebrum of Sanjiang cattle and Tibetan cattle,and 263 mRNAs and 1,807 lncRNAs co-differentially expressed in the cerebellum of Sanjiang cattle and Tibetan cattle comparison group,indicating that the number of differentially expressed genes in the cerebrum of Tibetan cattle and Sanjiang cattle were both less than that in cerebellum.The differentially expressed genes among Leiwuqi yak,Tibetan cattle and Sanjiang cattle were enriched for hypoxic adaptation-related signaling pathways,for instance,neural activity-receptor interactions,calcium signaling pathways,cGMPPKG signaling pathways,regulation of actin cytoskeleton,pancreatic secretions insulin secretion,renin secretion,adrenergic signaling in cardiomyocytes,vascular smooth muscle contraction,inositol phosphate metabolism,VEGF signaling pathway,metabolic pathway,p53 signaling pathway,and HIF-1 signaling pathway,etc.In addition,differentially expressed genes in cerebellum enriched more pathways related to hypoxic adaptation than that in cerebrum tissue.Significant enrichment of lncRNA target genes in Leiwuqi yak and common cattle groups(Tibetan cattle and Sanjiang cattle)is different in signalling pathways.The targets of Leiwuqi yak lncRNAs were enriched in the biological process(amino acids across the plasma membrane entrance,regulate gene expression,regulate macromolecular metabolism,etc.terms),the cell components(membrane-bound organelles,organelle membranes,cellulose and phosphatidylinositol-3-kinase complex,etc.terms),and the molecular function(L-ornithine transmembrane transporter activity,high affinity basic amino acid transmembrane transporter activity,organic cyclic compound binding,etc.terms),respectively.Pathway signaling pathways were significantly enriched in the complement and coagulation cascades(Q<0.05).However,the targets of cattle lncRNAs were enriched in biological process(neuropeptide catabolism process,regulation of angiotensin level in blood,regulation of angiotensin metabolism process,etc.terms),the cell components(dynein complex,transcriptional repressor complex,intracellular membrane-bound organelle,etc.terms),and the molecular function(phosphatidylinositol phosphate phosphatase activity,ligase activity,etc.terms),respectively.Pathway was significantly enriched in 26 signaling pathways such as Regulation of autophagy,AMPK signaling pathway,fat digestion and absorption,etc.In the hypoxic adaptationpathways,91 hypoxia-associated candidate genes were screened,then compared the expression level of highly expressed genes in different tissues,and the results showed that there was a significant differences between some tissues or populations(P<0.05).A group of genes were selected 8 for further validation by RT-qPCR,the results showed that the expression of ADRA1 A,MYLK,TNNC1,PRKCH,ACOX1,COX7 C,INPP4 and TPM3 genes in different tissues was consistent with the expression level of RNA-seq.Based on the results of high-throughput sequencing,the differentially expressed genes and related signaling pathways of lncRNA and mRNA in Leiwuqi yak,Tibetan cattle and Sanjiang cattle were screened for further exploring the molecular mechanism of hypoxic adaptation in yak.