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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Nature Publishing Group
2018
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ftumarylandhshsl:oai:archive.hshsl.umaryland.edu:10713/9048 2023-05-15T15:58:22+02:00 Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation Feng, D. Li, Q. Yu, H. 2018 http://hdl.handle.net/10713/9048 https://www.scopus.com/inward/record.uri?eid=2-s2.0-85040984977&doi=10.1038%2fs41598-018-19950-6&partnerID=40&md5=be001241eb62e490c277643111b94d0d https://doi.org/10.1038/s41598-018-19950-6 en_US eng Nature Publishing Group Scientific Reports https://www.scopus.com/inward/record.uri?eid=2-s2.0-85040984977&doi=10.1038%2fs41598-018-19950-6&partnerID=40&md5=be001241eb62e490c277643111b94d0d http://hdl.handle.net/10713/9048 doi:10.1038/s41598-018-19950-6 29362405 RNA Long Untranslated Neoplasms cancer tissues Article 2018 ftumarylandhshsl https://doi.org/10.1038/s41598-018-19950-6 2022-06-19T17:01:27Z 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. Copyright 2018 The Author(s). This study was supported by the grants from National Natural Science Foundation of China (31772843), Shandong Province (2016ZDJS06A06), and Industrial Development Project of Qingdao City (17-3-3-64-nsh). https://dx.doi.org/10.1038/s41598-018-19950-6 Article in Journal/Newspaper Crassostrea gigas UMB Digital Archive (University of Maryland, Baltimore) Scientific Reports 8 1 |
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Open Polar |
collection |
UMB Digital Archive (University of Maryland, Baltimore) |
op_collection_id |
ftumarylandhshsl |
language |
English |
topic |
RNA Long Untranslated Neoplasms cancer tissues |
spellingShingle |
RNA Long Untranslated Neoplasms cancer tissues Feng, D. Li, Q. Yu, H. Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation |
topic_facet |
RNA Long Untranslated Neoplasms cancer tissues |
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. Copyright 2018 The Author(s). This study was supported by the grants from National Natural Science Foundation of China (31772843), Shandong Province (2016ZDJS06A06), and Industrial Development Project of Qingdao City (17-3-3-64-nsh). https://dx.doi.org/10.1038/s41598-018-19950-6 |
format |
Article in Journal/Newspaper |
author |
Feng, D. Li, Q. Yu, H. |
author_facet |
Feng, D. Li, Q. Yu, H. |
author_sort |
Feng, D. |
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 |
publishDate |
2018 |
url |
http://hdl.handle.net/10713/9048 https://www.scopus.com/inward/record.uri?eid=2-s2.0-85040984977&doi=10.1038%2fs41598-018-19950-6&partnerID=40&md5=be001241eb62e490c277643111b94d0d https://doi.org/10.1038/s41598-018-19950-6 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_relation |
Scientific Reports https://www.scopus.com/inward/record.uri?eid=2-s2.0-85040984977&doi=10.1038%2fs41598-018-19950-6&partnerID=40&md5=be001241eb62e490c277643111b94d0d http://hdl.handle.net/10713/9048 doi:10.1038/s41598-018-19950-6 29362405 |
op_doi |
https://doi.org/10.1038/s41598-018-19950-6 |
container_title |
Scientific Reports |
container_volume |
8 |
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1 |
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1766394104618418176 |