基于高通量转录组测序阿尔巴斯型绒山羊绒毛生长周期差异表达基因分析

Study on differentially expressed genes in the cycle of follicle growth of Arbas cashmere goat based on transcriptomes with high-throughput RNA-seq technology

关键词:  绒山羊  转录组  差异表达基因  皮肤  绒毛生长周期

Key words:  caprine  transcriptomes  differentially expressed genes  skin  cycle of follicle growth

摘要:

为研究绒山羊绒毛生长周期内皮肤基因表达规律以及皮肤差异表达基因的挖掘，采用Illumina HiSeq^TM 2000高通量转录组测序平台RNA-Seq技术，对3只成年雌性阿尔巴斯型内蒙古绒山羊全年12个月的皮肤样本进行转录组测序，将无参考基因组de novo拼接组装的unigene运用Nr，GO，COG以及KEGG数据库进行比对注释，并进行差异基因在全年各月份间的变化规律分析。结果显示，测序获得的unigene数为105 854条，比对注释基因55 541个，其中共有51 078条转录本进行了GO注释，21 189条转录本在COG数据库分析得到注释，26 201条预测基因KEGG数据库比对成功。其中皮肤基因GO注释在生物学功能分类中，细胞过程、代谢过程、生物学调控、生物功能调控以及刺激应答方面注释到的转录本比例最大；在分子功能分类中，结合以及催化活性作用方面注释到的转录本比例最大；通过COG数据库的比对注释，看到皮肤表达基因的同源蛋白功能主要集中在基因转录、翻译后修饰、和信号传导机制方面，反而在同工酶转运和代谢、细胞动力、二级代谢生物合成、转运和催化以及核结构方面注释到的基因极少；皮肤转录组数据与KEGG数据库比对，得到皮肤相关转录本较为富集的几条通路分别为MAPK signaling pathway，Wnt signaling pathway，Notch signaling pathway，Hedgehog signaling pathway，TGF-β signaling pathway，JAK-STAT signaling pathway以及Focal signaling pathway；通过绒山羊不同月份皮肤转录组测序数据进行差异基因分析，得出绒山羊全年皮肤生长周期中基因差异变化规律为绒山羊全年皮肤共有4次较为剧烈的基因差异变化，第1次发生在2月与3月之间，第2次发生在3月与4月之间，第3次发生在6月与7月之间，第4次发生在10月与11月之间，前2次出现的基因差异变化较后2次剧烈得多，说明绒山羊绒毛生长启动时基因变化剧烈，而绒毛生长到休止时的皮肤基因变化较为缓和，是一个基因缓慢变化的过程。

Abstract:

The objectives of this study were to find the expression pattern of the caprine skin genes and investigate the differentially expressed genes in during follicle growth cycle.Skin samples of three female Arbas cashmere goats were colltected at the early stage of each month in whole year.mRNAs of samples belong different month were extract respectively,and transcriptomes were analyzed by Illumina HiSeq^TM 2000 high-throughput RNA sequencing.Unigenes with no genome reference were annotated using BLAST search against Nr,GO and KEGG databases.And the expression patterns of differentially expressed genes of different month were analyzed.The result showed that:A total of 55 541 genes were confirmed among 105 854 unigenes discovered.51 078 unigenes were annotated by GO,21 189 unigenes were annotated by COG and 26 201 unigenes was annotated by KEGG database,respectively.Unigenes annotated were found mostly involving in cellular process,metabolic process,biological regulation,regulation of biological process and response to stimulus.Unigenes annotated were mainly with binding and catalytic activity.And by comparison of BLAST with COG database,it was found that the skin genes discovered focused on gene transcription,post-translation modification and signaling mechanisms and were very rare involved in isoenzyme transport and metabolism,cell power,biosynthesis of secondary metabolites,transport and catalytic and nuclear structure.The result from KEGG database annotation showed that skin genes were enrich in MAPK signaling pathway,Wnt signaling pathway,notch signaling pathway,hedgehog signaling pathway,TGF-β signaling pathway,JAK-STAT signaling pathway and focal signaling pathway.By the analysis of transcriptome data,the differentially expressed genes in different month skin's during whole year displayed four times expression changes:The first change occurred between February and March,the second change occurred between March and April,the third change occurred June and July,and the last gene expression change occurred between October and November.The changes of first two are greater than last two,indicating that during the follicle early growth,the skin genes had greater expression change.And the skin genes expression change of follicle growth in the catagen and telogen were smoother and moderate.