The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation
Abstract Background 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...
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| Format: | Article |
| Language: | English |
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BMC
2021-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-020-07313-3 |
| _version_ | 1828969602286092288 |
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| author | Longsheng Xing Yu Xi Xi Qiao Cong Huang Qiang Wu Nianwan Yang Jianyang Guo Wanxue Liu Wei Fan Fanghao Wan Wanqiang Qian |
| author_facet | Longsheng Xing Yu Xi Xi Qiao Cong Huang Qiang Wu Nianwan Yang Jianyang Guo Wanxue Liu Wei Fan Fanghao Wan Wanqiang Qian |
| author_sort | Longsheng Xing |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusions 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. |
| first_indexed | 2024-12-14T12:33:55Z |
| format | Article |
| id | doaj.art-48a52ecff9734efc97e76df4c913b26c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T12:33:55Z |
| publishDate | 2021-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-48a52ecff9734efc97e76df4c913b26c2022-12-21T23:01:06ZengBMCBMC Genomics1471-21642021-01-0122111710.1186/s12864-020-07313-3The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulationLongsheng Xing0Yu Xi1Xi Qiao2Cong Huang3Qiang Wu4Nianwan Yang5Jianyang Guo6Wanxue Liu7Wei Fan8Fanghao Wan9Wanqiang Qian10Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesAbstract Background 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. Results 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. Conclusions 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.https://doi.org/10.1186/s12864-020-07313-3Long noncoding RNAConservationSyntenyTranscriptional regulationCydia pomonella |
| spellingShingle | Longsheng Xing Yu Xi Xi Qiao Cong Huang Qiang Wu Nianwan Yang Jianyang Guo Wanxue Liu Wei Fan Fanghao Wan Wanqiang Qian The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation BMC Genomics Long noncoding RNA Conservation Synteny Transcriptional regulation Cydia pomonella |
| title | The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation |
| title_full | The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation |
| title_fullStr | The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation |
| title_full_unstemmed | The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation |
| title_short | The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation |
| title_sort | landscape of lncrnas in cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation |
| topic | Long noncoding RNA Conservation Synteny Transcriptional regulation Cydia pomonella |
| url | https://doi.org/10.1186/s12864-020-07313-3 |
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