基于转录组测序的半滑舌鳎长链非编码RNA的初步鉴定与分析

Identification and characterization of long non-coding RNAs from Cynoglossus semilaevis based on transcriptomics

摘要:

以抗病家系与易感家系半滑舌鳎为材料，进行哈维弧菌感染实验，并对易感家系感染前（CsSU）、易感家系感染后（CsSC）、抗病家系感染前（CsRU）、抗病家系感染后（CsRC）4组进行转录组测序，根据RNA-seq数据挖掘半滑舌鳎长链非编码RNA信息；通过生物信息学分析，筛选出与抗哈维弧菌病相关的差异长链非编码RNA（long non-coding RNA， lncRNA）。结果显示，共识别出4 584个lncRNA座位，包含5 714个转录本；其基本特征与编码基因的比较分析，lncRNA的GC含量低于编码基因，单外显子基因数多于编码基因，转录本的平均长度长于编码基因，基因表达量低于编码基因。对4组样品进行两两比较（CsRU vs CsSU、CsRC vs CsSC、CsRC vs CsRU、CsSC vs CsSU）分别筛选出818、813、261、140个差异表达lncRNA，其中CsRU与CsSU之间、CsRC与CsSC之间lncRNA数目差异最多，通过聚类分析确定了各实验组的表达模式之间的联系，CsRU与CsSU之间的表达模式最为相近。通过共表达分析，预测出lncRNA和274个编码基因可能存在14 539种相互关系，并进行了功能注释，进而筛选出7个关键lncRNA。qRT-PCR结果显示，差异表达lncRNAs的表达模式和转录组数据得到的基本一致。研究结果为揭示lncRNA在半滑舌鳎抗哈维弧菌免疫调控反应中的作用提供重要的参考数据。

Abstract:

Long non-coding RNA (lncRNA) plays an important role in the regulation of epigenetics, transcription, and post-transcription. To understand the regulation mechanism of immune response to Vibrio harveyi, we performed lncRNA identification and differential expression analysis from RNA-seq data. We obtained a total of 4 584 lncRNA loci, containing 5 714 transcripts in this study. The comparison of basic characteristics between lncRNA and the coding gene showed that the GC content of lncRNAs was lower than that of coding genes, and single exon genes number was greater than that of coding genes, and the average transcripts length of lncRNAs was longer than that of coding genes, and the average expression of lncRNAs was slightly lower than coding genes. We screened 818, 813, 261 and 140 differentially expressed lncRNAs by differential expression analysis in four comparisons of Cynoglossus semilaevis groups (CsRU vs CsSU, CsRC vs CsSC, CsRC vs CsRU, CsSC vs CsSU), respectively. Additionally, we preliminarily analyzed the expression patterns and the relationship of differential expression of lncRNAs from those four groups. Through co-expression analysis, a total of 14 539 types of interaction relationships were detected between 285 lncRNA and 274 coding genes. We performed GO annotation and screened 7 key lncRNA. The qRT-PCR confirmed that the expression patterns of lncRNAs were consistent with their expression levels bases on transcriptome data. This study provides some of reference data for studying the role of lncRNA in the immune response against V. harveyi.