Cargando…
The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation
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...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7786964/ https://www.ncbi.nlm.nih.gov/pubmed/33402093 http://dx.doi.org/10.1186/s12864-020-07313-3 |
_version_ | 1783632734598463488 |
---|---|
author | Xing, Longsheng Xi, Yu Qiao, Xi Huang, Cong Wu, Qiang Yang, Nianwan Guo, Jianyang Liu, Wanxue Fan, Wei Wan, Fanghao Qian, Wanqiang |
author_facet | Xing, Longsheng Xi, Yu Qiao, Xi Huang, Cong Wu, Qiang Yang, Nianwan Guo, Jianyang Liu, Wanxue Fan, Wei Wan, Fanghao Qian, Wanqiang |
author_sort | Xing, Longsheng |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7786964 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-77869642021-01-07 The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation Xing, Longsheng Xi, Yu Qiao, Xi Huang, Cong Wu, Qiang Yang, Nianwan Guo, Jianyang Liu, Wanxue Fan, Wei Wan, Fanghao Qian, Wanqiang BMC Genomics Research Article 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. BioMed Central 2021-01-05 /pmc/articles/PMC7786964/ /pubmed/33402093 http://dx.doi.org/10.1186/s12864-020-07313-3 Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Xing, Longsheng Xi, Yu Qiao, Xi Huang, Cong Wu, Qiang Yang, Nianwan Guo, Jianyang Liu, Wanxue Fan, Wei Wan, Fanghao Qian, Wanqiang The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation |
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 | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7786964/ https://www.ncbi.nlm.nih.gov/pubmed/33402093 http://dx.doi.org/10.1186/s12864-020-07313-3 |
work_keys_str_mv | AT xinglongsheng thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT xiyu thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT qiaoxi thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT huangcong thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT wuqiang thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT yangnianwan thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT guojianyang thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT liuwanxue thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT fanwei thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT wanfanghao thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT qianwanqiang thelandscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT xinglongsheng landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT xiyu landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT qiaoxi landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT huangcong landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT wuqiang landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT yangnianwan landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT guojianyang landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT liuwanxue landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT fanwei landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT wanfanghao landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation AT qianwanqiang landscapeoflncrnasincydiapomonellaprovidesinsightsintotheirsignaturesandpotentialrolesintranscriptionalregulation |