Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation
Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and have drawn extensive attention in the past few years. However, lncRNAs remain poorly understood about expression and roles in Crassostrea gigas, a potential model organism for marine molluscan studies. Here, we sys...
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ftpubmed:oai:pubmedcentral.nih.gov:5780484 2023-05-15T15:58:06+02:00 Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation Feng, Dandan Li, Qi Yu, Hong Kong, Lingfeng Du, Shaojun 2018-01-23 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780484/ http://www.ncbi.nlm.nih.gov/pubmed/29362405 https://doi.org/10.1038/s41598-018-19950-6 en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780484/ http://www.ncbi.nlm.nih.gov/pubmed/29362405 http://dx.doi.org/10.1038/s41598-018-19950-6 © The Author(s) 2018 Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/. CC-BY Article Text 2018 ftpubmed https://doi.org/10.1038/s41598-018-19950-6 2018-02-11T01:11:57Z Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and have drawn extensive attention in the past few years. However, lncRNAs remain poorly understood about expression and roles in Crassostrea gigas, a potential model organism for marine molluscan studies. Here, we systematically identified lncRNAs in the mantles of C. gigas from four full-sib families characterized by white, black, golden, and partially pigmented shell. Using poly(A)-independent and strand-specific RNA-seq, a total of 441,205,852 clean reads and 12,243 lncRNA transcripts were obtained. LncRNA transcripts were relatively short with few exons and low levels of expression in comparison to protein coding mRNA transcripts. A total of 427 lncRNAs and 349 mRNAs were identified to differentially express among six pairwise groups, mainly involving in biomineralization and pigmentation through functional enrichment. Furthermore, a total of 6 mRNAs and their cis-acting lncRNAs were predicted to involve in synthesis of melanin, carotenoid, tetrapyrrole, or ommochrome. Of them, chorion peroxidase and its cis-acting lincRNA TCONS_00951105 are implicated in playing an essential role in the melanin synthetic pathway. Our studies provided the first systematic characterization of lncRNAs catalog expressed in oyster mantle, which may facilitate understanding the molecular regulation of shell colour diversity and provide new insights into future selective breeding of C. gigas for aquaculture. Text Crassostrea gigas PubMed Central (PMC) Scientific Reports 8 1 |
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Article Feng, Dandan Li, Qi Yu, Hong Kong, Lingfeng Du, Shaojun Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation |
topic_facet |
Article |
description |
Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and have drawn extensive attention in the past few years. However, lncRNAs remain poorly understood about expression and roles in Crassostrea gigas, a potential model organism for marine molluscan studies. Here, we systematically identified lncRNAs in the mantles of C. gigas from four full-sib families characterized by white, black, golden, and partially pigmented shell. Using poly(A)-independent and strand-specific RNA-seq, a total of 441,205,852 clean reads and 12,243 lncRNA transcripts were obtained. LncRNA transcripts were relatively short with few exons and low levels of expression in comparison to protein coding mRNA transcripts. A total of 427 lncRNAs and 349 mRNAs were identified to differentially express among six pairwise groups, mainly involving in biomineralization and pigmentation through functional enrichment. Furthermore, a total of 6 mRNAs and their cis-acting lncRNAs were predicted to involve in synthesis of melanin, carotenoid, tetrapyrrole, or ommochrome. Of them, chorion peroxidase and its cis-acting lincRNA TCONS_00951105 are implicated in playing an essential role in the melanin synthetic pathway. Our studies provided the first systematic characterization of lncRNAs catalog expressed in oyster mantle, which may facilitate understanding the molecular regulation of shell colour diversity and provide new insights into future selective breeding of C. gigas for aquaculture. |
format |
Text |
author |
Feng, Dandan Li, Qi Yu, Hong Kong, Lingfeng Du, Shaojun |
author_facet |
Feng, Dandan Li, Qi Yu, Hong Kong, Lingfeng Du, Shaojun |
author_sort |
Feng, Dandan |
title |
Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation |
title_short |
Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation |
title_full |
Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation |
title_fullStr |
Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation |
title_full_unstemmed |
Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation |
title_sort |
transcriptional profiling of long non-coding rnas in mantle of crassostrea gigas and their association with shell pigmentation |
publisher |
Nature Publishing Group UK |
publishDate |
2018 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780484/ http://www.ncbi.nlm.nih.gov/pubmed/29362405 https://doi.org/10.1038/s41598-018-19950-6 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780484/ http://www.ncbi.nlm.nih.gov/pubmed/29362405 http://dx.doi.org/10.1038/s41598-018-19950-6 |
op_rights |
© The Author(s) 2018 Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/s41598-018-19950-6 |
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