Genome-wide identification of lncRNAs and their potential association with cold stress in tilapia

Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and cold-stress related expression of lncRNAs in tilapia is still limited. Genome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 126 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 35,328 high-confidence set of lncRNAs were detected from the RNA-seq datasets. 5,939 lncRNAs (~17%) were overlapped with 13,450 mRNA genes with at least one basepair of overlap. We observed an average correlation coefficient of 0.06 for all lncRNA-mRNA pairs, 0.09 for lncRNA-lncRNA pairs and 0.12 for mRNA-mRNA pairs. These correlation data is far less than that for the overlapped lncRNA and mRNA pairs (r = 0.22). Weighted correlation network analysis of the lncRNA and mRNA datasets from 14 tissues identified 30 modules and many interesting genes existed, e.g., SLC13A1, GGT1, GRHL1, GATA3, RE11, CLDN4L, CLDN8, OCLN. Differential expression (DE) analysis identified 923 and 246 DE lncRNAs in brain and heart, respectively. miRNA-lncRNA interaction analysis detected 923 lncRNAs containing motifs with sequence complementary to 462 miRNAs in brain, and 246 lncRNAs showing interaction with 462 miRNAs in heart. This study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will elucidate their roles in regulating stress-related adaptation.长链非编码RNA（long noncoding RNAs，LncRNAs）在基础生物学过程中发挥重要作用。然而，目前关于罗非鱼基因组范围内长链非编码RNA的分布模式以及冷胁迫相关表达特征的认知仍较为有限。本研究借助生物信息学工具，对罗非鱼基因组中的长链非编码RNA开展了全基因组范围的鉴定工作。本研究分析了126组RNA测序（RNA sequencing，RNA-seq）数据集，这些数据集一部分由本实验室生成，另一部分从NCBI数据库中获取。最终从这些RNA测序数据集中共鉴定得到35328条高置信度长链非编码RNA。其中5939条长链非编码RNA（约占总数的17%）与13450个信使RNA（messenger RNA，mRNA）基因存在至少1个碱基的重叠区域。我们观察到，所有长链非编码RNA-信使RNA对的平均相关系数为0.06，长链非编码RNA-长链非编码RNA对的平均相关系数为0.09，而信使RNA-信使RNA对的平均相关系数为0.12。上述相关系数均远低于存在重叠区域的长链非编码RNA与信使RNA对的相关系数（r=0.22）。本研究对来自14种组织的长链非编码RNA和信使RNA数据集开展加权相关网络分析，共鉴定得到30个模块，并发现了多个功能值得关注的基因，例如SLC13A1、GGT1、GRHL1、GATA3、RE11、CLDN4L、CLDN8以及OCLN。差异表达（differential expression，DE）分析共鉴定得到923条在脑组织中差异表达的长链非编码RNA，以及246条在心脏组织中差异表达的长链非编码RNA。微小RNA（microRNA，miRNA）-长链非编码RNA互作分析显示，在脑组织中有923条长链非编码RNA含有与462种微小RNA序列互补的基序，而在心脏组织中有246条长链非编码RNA可与462种微小RNA发生互作。本研究为后续解析罗非鱼基因组中长链非编码RNA的分子基础提供了宝贵的研究资源。后续针对长链非编码RNA的功能分析，将进一步阐明其在调控胁迫适应过程中发挥的作用。