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Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection

Large-scale transcription studies have revealed numerous lncRNAs (long non-coding RNAs). lncRNAs have been proposed to participate in the regulation of a diverse range of biological processes, including transcriptional regulation. Although lncRNAs have attracted increasing attention, the studies in...

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Autores principales: Zhang, Xinyi, Zhou, Tao, Chen, Baohua, Bai, Huaqiang, Bai, Yulin, Zhao, Ji, Pu, Fei, Wu, Yidi, Chen, Lin, Shi, Yue, Ke, Qiaozhen, Zheng, Weiqiang, Chen, Jia, Xu, Peng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7689269/
https://www.ncbi.nlm.nih.gov/pubmed/33281881
http://dx.doi.org/10.3389/fgene.2020.590475
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author Zhang, Xinyi
Zhou, Tao
Chen, Baohua
Bai, Huaqiang
Bai, Yulin
Zhao, Ji
Pu, Fei
Wu, Yidi
Chen, Lin
Shi, Yue
Ke, Qiaozhen
Zheng, Weiqiang
Chen, Jia
Xu, Peng
author_facet Zhang, Xinyi
Zhou, Tao
Chen, Baohua
Bai, Huaqiang
Bai, Yulin
Zhao, Ji
Pu, Fei
Wu, Yidi
Chen, Lin
Shi, Yue
Ke, Qiaozhen
Zheng, Weiqiang
Chen, Jia
Xu, Peng
author_sort Zhang, Xinyi
collection PubMed
description Large-scale transcription studies have revealed numerous lncRNAs (long non-coding RNAs). lncRNAs have been proposed to participate in the regulation of a diverse range of biological processes, including transcriptional regulation. Although lncRNAs have attracted increasing attention, the studies in large yellow croaker (Larimichthys crocea) are still rare, and they lack systematic analysis. In this study, 101 RNA-seq datasets varied in ages, sexes, and tissues were retrieved from the NCBI database to generate a comprehensive catalog of large yellow croaker transcriptome database. A set of 14,599 high-confidence lncRNAs from 13,673 loci were identified and characterized. Furthermore, RNA-seq datasets obtained from the infection of C. irritans were employed to investigate the differential expression pattern of lncRNAs and analyze potential biological functions. A total of 77 differentially expressed lncRNAs targeting to 567 protein-coding genes were identified by using expression analysis. Several immune genes, including TLR5, CD2AP, and MMP9, were highlighted. With GO enrichment and KEGG pathway analysis, the immune-related terms or pathways were enriched. This study created a comprehensive dataset of lncRNAs for large yellow croaker, which would be helpful for the researches of functional roles of lncRNAs in large yellow croaker.
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spelling pubmed-76892692020-12-04 Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection Zhang, Xinyi Zhou, Tao Chen, Baohua Bai, Huaqiang Bai, Yulin Zhao, Ji Pu, Fei Wu, Yidi Chen, Lin Shi, Yue Ke, Qiaozhen Zheng, Weiqiang Chen, Jia Xu, Peng Front Genet Genetics Large-scale transcription studies have revealed numerous lncRNAs (long non-coding RNAs). lncRNAs have been proposed to participate in the regulation of a diverse range of biological processes, including transcriptional regulation. Although lncRNAs have attracted increasing attention, the studies in large yellow croaker (Larimichthys crocea) are still rare, and they lack systematic analysis. In this study, 101 RNA-seq datasets varied in ages, sexes, and tissues were retrieved from the NCBI database to generate a comprehensive catalog of large yellow croaker transcriptome database. A set of 14,599 high-confidence lncRNAs from 13,673 loci were identified and characterized. Furthermore, RNA-seq datasets obtained from the infection of C. irritans were employed to investigate the differential expression pattern of lncRNAs and analyze potential biological functions. A total of 77 differentially expressed lncRNAs targeting to 567 protein-coding genes were identified by using expression analysis. Several immune genes, including TLR5, CD2AP, and MMP9, were highlighted. With GO enrichment and KEGG pathway analysis, the immune-related terms or pathways were enriched. This study created a comprehensive dataset of lncRNAs for large yellow croaker, which would be helpful for the researches of functional roles of lncRNAs in large yellow croaker. Frontiers Media S.A. 2020-11-12 /pmc/articles/PMC7689269/ /pubmed/33281881 http://dx.doi.org/10.3389/fgene.2020.590475 Text en Copyright © 2020 Zhang, Zhou, Chen, Bai, Bai, Zhao, Pu, Wu, Chen, Shi, Ke, Zheng, Chen and Xu. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Zhang, Xinyi
Zhou, Tao
Chen, Baohua
Bai, Huaqiang
Bai, Yulin
Zhao, Ji
Pu, Fei
Wu, Yidi
Chen, Lin
Shi, Yue
Ke, Qiaozhen
Zheng, Weiqiang
Chen, Jia
Xu, Peng
Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection
title Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection
title_full Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection
title_fullStr Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection
title_full_unstemmed Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection
title_short Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection
title_sort identification and expression analysis of long non-coding rna in large yellow croaker (larimichthys crocea) in response to cryptocaryon irritans infection
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7689269/
https://www.ncbi.nlm.nih.gov/pubmed/33281881
http://dx.doi.org/10.3389/fgene.2020.590475
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