| In this study, the lung tissues from the Mai-Wa yak from Aba region of Sichuan and cattle was chosen as research subjects. Illumina HiSeq TM2000 platform was used to carry out the sequencing in depth. Furthermore, we compare the transcriptome from yak and cattle. The obtained clean reads were compared with yak genome and related reference genes. At the same time, structural optimization analysis, alternative splicing analysis, new transcripts predict, SNP loci predict, GO and KEGG Pathway enrichment analysis for differentially expressed genes were carried out.1. After removing the linker sequence, empty sequence some data of low quality, 51,641,282 clean reads were obtained from the total mRNA of yak lung tissue.2. The comparative analysis shows that a total of 31,898,650 reads were Mapped on the yak reference genome, of which unique match sequence were 30,021,903(58.14% of Total Mapped Reads). Besides, there were 18,409,161 reads mapped to the reference gene, of which unique match sequence were 17,626,475 reads(34.13%of Total Mapped Reads). 3. Structure optimization analysis showed that a total of 8123 genes occurred extending in the original location on genomic of yak, including the 4719 genes 5 ’end of extending and 3404 genes 3’ end of extending. 4. New forecasting transcripts showed a total of 7059 new transcripts was found in yak lung transcriptome, distributing 180 ~ 14884 bp. this result provides data for further tap the potential new gene annotation of yak especially with the altitude hypoxia adaptation. 5. The results of Alternative splicing analysis and SNP analysis showed that yak has been involved in more than a total of 4097 genes on alternative splicing, of which Intron retentio were accounted for the largest proportion, followed by exon skipping and alternative 3’ splice site. SOAPsnp was applied to detect single nucleotide polymorphisms between samples, the results of SNP analysis showed that there may be 70,601 single nucleotide polymorphisms sites presenced on the yak genome. 6. Screening of differentially expressed genes and GO and KEGG Pathway enrichment analysis showed that a total of 16,815 yak lung tissue genes, compared with cattle, yak number of genes differentially expressed in lung tissue has 1618, including 1037 gene expression is raised, 581 genes showed reduced. Of differentially expressed genes in the GO enrichment analysis further showed that cellular components involving a total of 418 classified section entries focus on the analysis found that the most enriched plasma membrane accounts for a significant proportion of part(4/10) of its Top10, followed by the extracellular domain part(3/10) and intracellular transport lipoprotein related entries(3/10).KEGG annotation results showed that a total of 1412 genes involved in pathways, of which the top 10 pathway enrichment in the complement and coagulation cascade most enrichment, followed by Metabolism of xenobiotics by cytochrome P450 and Drug metabolism-cytochrome P450.This study successfully gained the yak lung transcriptome by RNA-Seq technology. At the same time, we compared the lung transcriptome of cattle and the yaks in order to understand yaks’ special adaptive mechanism to low oxygen. This study will provide important foundation and platform for the further research of hypoxia adaptation in yak and other plateau animal and provides a basis for the prevention and treatment of human and animal lung-related diseases especially hypoxic injury caused by hypoxia. Moreover, this study also provides valuable data for further improvement of yak genome database. |
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