Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
BMC Genomics. 2021 Jan 5;22(1):4. doi: 10.1186/s12864-020-07313-3.
Long noncoding RNAs (lncRNAs) have emerged as an important class of transcriptional regulators in cellular processes. The past decades have witnessed great progress in lncRNA studies in a variety of organisms. The codling moth (Cydia pomonella L.) is an important invasive insect in China. However, the functional impact of lncRNAs in this insect remains unclear. In this study, an atlas of codling moth lncRNAs was constructed based on publicly available RNA-seq datasets.
In total, 9875 lncRNA transcripts encoded by 9161 loci were identified in the codling moth. As expected, the lncRNAs exhibited shorter transcript lengths, lower GC contents, and lower expression levels than protein-coding genes (PCGs). Additionally, the lncRNAs were more likely to show tissue-specific expression patterns than PCGs. Interestingly, a substantial fraction of the lncRNAs showed a testis-biased expression pattern. Additionally, conservation analysis indicated that lncRNA sequences were weakly conserved across insect species, though additional lncRNAs with homologous relationships could be identified based on synteny, suggesting that synteny could be a more reliable approach for the cross-species comparison of lncRNAs. Furthermore, the correlation analysis of lncRNAs with neighbouring PCGs indicated a stronger correlation between them, suggesting potential cis-acting roles of these lncRNAs in the regulation of gene expression.
Taken together, our work provides a valuable resource for the comparative and functional study of lncRNAs, which will facilitate the understanding of their mechanistic roles in transcriptional regulation.
长非编码 RNA（lncRNA）已成为细胞过程中一类重要的转录调控因子。在过去的几十年中，在各种生物体中，lncRNA 的研究取得了巨大的进展。桃小食心虫（Cydia pomonella L.）是中国一种重要的入侵性昆虫。然而，lncRNAs 在这种昆虫中的功能影响尚不清楚。在本研究中，基于公共 RNA-seq 数据集构建了桃小食心虫 lncRNA 图谱。
总共鉴定到 9875 个由 9161 个基因座编码的 lncRNA 转录本。与预期一致，lncRNAs 的转录本长度较短，GC 含量较低，表达水平也低于蛋白质编码基因（PCGs）。此外，lncRNAs 比 PCGs 更有可能表现出组织特异性表达模式。有趣的是，相当一部分 lncRNAs 表现出偏向睾丸的表达模式。此外，保守性分析表明，尽管可以基于基因同线性鉴定出具有同源关系的额外 lncRNA，但昆虫物种之间的 lncRNA 序列保守性较弱，这表明基因同线性可能是跨物种比较 lncRNA 的更可靠方法。此外，lncRNA 与邻近 PCGs 的相关性分析表明它们之间存在更强的相关性，这表明这些 lncRNA 在基因表达调控中可能具有顺式作用。
总之，我们的工作为 lncRNA 的比较和功能研究提供了有价值的资源，这将有助于理解它们在转录调控中的机制作用。
