Comparative Transcriptome Analysis Of Ovary In Yak By RNA-Seq

As a Chinese endemic species,Bos grunniens is very important to tibetan herdsman.Compared with cattle, the reproductive performance of yak is lower.So the study on reproductive performance of yak is conducive to the economic development of the Tibet plateau.Ovary is the female animal’s reproductive organs and previous researches on Yak ovary usually focused on anatomy and genetic level.In this study, we successfully extracted trace RNA of yak and cattle ovary. Then RNA-Seq technology were used to depth transcriptome sequencing by Illumina Hi SeqTM2000 platform.Lastly, the obtained Clean reads were compared with yak genome and related reference genes for analysis.The results were below:1. After remove the linker sequence, reading the empty sequence and the low quality of deep sequencing dates, 53,653,032 clean reads were obtained from the total m RNA of yak ovary tissue.The clean reads of cattle ovary tissue is 54,855,396.2. The alignment analysis results of the reference genome indicated a total of 33168751 genes from yak ovary were mapped and 6321 novel transcripts that could be positioned back to the yak genome were obtained; The length of new transcripts varies from 145 bp to 14885 bp, 2264 novel transcripts was calculated to be able express protein.3. Structure optimization analysis showed that a total of 7340 genes occurred extending in the original location on genomic of yak, including the 4241 genes 5 ’end of extending and 3099 genes 3’ end of extending.4. The analysis of transcript alternative splicing indentified that a total of 3734 genes in yak overy are involved in alternative splicing.The results of SNP analysis showed that there may be 70,601 single nucleotide polymorphisms sites presenced on the yak genome.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.which Intron retentio were accounted for the largest proportion, followed by exon skipping and alternative 3’ splice site. Use SOAPsnp(Li, 2009) 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. Compared with cattle, there exist 661 genes with increased m RNA level and 646 genes with decreased m RNA level in yak overy. GO enrichment analysis showed that those genes with significantly different expression level were enriched above the three main categories(Molecular function, Cellular component, and Cellular process). The KEGG enrichment analysis showed that there were 1412 genes involved in 247 pathways, of which the ‘Complement and coagulation cascades’ was most enriched, the next is ‘Metabolism of xenobiotics by cytochrome P450’, and ‘Circadian rhythm-mammal’ is enriched.In summary, we obtained the transcriptome of yak and cattle overy by RNA-seq, which help us complete the information of yak genome and dig some potential new genes. By compare with the cattle transcriptome,the differences in reproductive performance of yak and cattle was explored from transcriptomics perspective.This study revealed propagation properties of Yak from the perspective of molecular and provided valuable data for further improvement of yak genome database.