绒山羊皮肤全长转录组测序及生物信息学分析

Sequencing and bioinformatics analysis of the full-length transcriptome of cashmere goat skin

为能够更精准地得到绒山羊皮肤mRNA全长序列和完整结构信息,并对新基因和Iso-form进行更全面的分析以对绒山羊转录组数据进行补充,以绒山羊作为试验动物,使用SMRT测序技术,对绒山羊皮肤组织混合样品进行全长转录组测序,并使用TransDecoder、Astalavista和Cytoscape等分析工具对其编码区序列及其对应氨基酸序列、可变剪接类型以及基因功能富集进行预测分析。结果表明:1)测序共获得42.41Gb clean data的数据,CCS(Circular consensus sequencing)591585条,其中全长非嵌合序列466058条。2)共鉴定出6166个新基因,55875条新转录本,SSR(Simple sequence repeat)66951个、ORF(Open reading frame)序列39346条、TF(Transcription factors)5641个及10927个lncRNA,并完成49573条新转录本的功能注释。3)鉴定出25717种可变剪接,其中内含子保留为主要的剪接方式,基于功能富集分析结果和可变剪接位点信息发现黑素皮质素1受体(Melanocortin 1receptor,MC1R)与微管蛋白3类(Tubulin-β-Ⅲ,TUBB3)可发生可变剪接,共用TUBB3第一外显子。鉴定的lncRNA中新lncRNA 8251个,主要类型为内含子lncRNA。本研究更精准地得到了绒山羊皮肤mRNA全长序列及完整结构信息,为进一步研究绒山羊皮肤基因结构及互作机理奠定基础,同时为绒山羊基因组资源进行了数据补充。

In order to more accurately obtain the full-length mRNA sequences and complete structural information of cashmere goat skin,and conduct more comprehensive research on new genes and ISO form,and supplement the cashmere goat transcriptome data,cashmere goat was used as an experimental animal in the study.The full-length transcriptome of mixed samples of cashmere goat skin tissue using SMRT sequencing technology as test animals were sequenced.The sequences of coding regions and their corresponding amino acid sequences,variable splice types,and functional enrichment were predicted by using TransDecoder,Astalavista,Cytoscape and other analysis tools.The results showed that:1)A total of 42.41Gb of clean data were obtained by sequencing,with 591585CCS(Circular consensus sequencing)sequences,including 466058full-length non-chimeric sequences.2)A total of 6166new genes,55875new transcripts,66951 SSR(Simple Sequence Repeat),39346 ORF(Open Reading Frame)sequences,5641TF(Transcription Factors)and 10927lncRNAs were identified,and the functional annotation of49573new transcripts were annotated.3)Based on the results of functional enrichment analysis and variable splice site information,we found that melanocortin 1receptor(MC1R)and microtubulin class 3(Tubulin-β-Ⅲ,TUBB3)could undergo variable splicing and share TUBB3first exon.There were 8251new lncRNAs identified,and the main type was intronic lncRNA.In conclusion,the full-length sequence and complete structural information of the mRNA of the skin of cashmere goat is obtained,which lays the foundation for further study of the gene structure and interaction mechanism of the skin of cashmere goat.At the same time,the data are supplemented for cashmere goat genome resources.