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Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress

Drought stress is one of the most severe abiotic stresses that restrict global crop production. Long non-coding RNAs (lncRNAs) have been proved to play a key role in response to drought stress. However, genome-wide identification and characterization of drought-responsive lncRNAs in sugar beet is st...

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Autores principales: Zou, Chunlei, Guo, Zhiqiang, Zhao, Shanshan, Chen, Jishuai, Zhang, Chunlai, Han, Haoran
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9971629/
https://www.ncbi.nlm.nih.gov/pubmed/36866366
http://dx.doi.org/10.3389/fpls.2023.1118011
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author Zou, Chunlei
Guo, Zhiqiang
Zhao, Shanshan
Chen, Jishuai
Zhang, Chunlai
Han, Haoran
author_facet Zou, Chunlei
Guo, Zhiqiang
Zhao, Shanshan
Chen, Jishuai
Zhang, Chunlai
Han, Haoran
author_sort Zou, Chunlei
collection PubMed
description Drought stress is one of the most severe abiotic stresses that restrict global crop production. Long non-coding RNAs (lncRNAs) have been proved to play a key role in response to drought stress. However, genome-wide identification and characterization of drought-responsive lncRNAs in sugar beet is still lacking. Thus, the present study focused on analyzing lncRNAs in sugar beet under drought stress. We identified 32017 reliable lncRNAs in sugar beet by strand-specific high-throughput sequencing. A total of 386 differentially expressed lncRNAs (DElncRNAs) were found under drought stress. The most significantly upregulated and downregulated lncRNAs were TCONS_00055787 (upregulated by more than 6000 fold) and TCONS_00038334 (downregulated by more than 18000 fold), respectively. Quantitative real-time PCR results exhibited a high concordance with RNA sequencing data, which conformed that the expression patterns of lncRNAs based on RNA sequencing were highly reliable. In addition, we predicted 2353 and 9041 transcripts that were estimated to be the cis- and trans-target genes of the drought-responsive lncRNAs. As revealed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the target genes of DElncRNAs were significantly enriched in organelle subcompartment, thylakoid, endopeptidase activity, catalytic activity, developmental process, lipid metabolic process, RNA polymerase activity, transferase activity, flavonoid biosynthesis and several other terms associated with abiotic stress tolerance. Moreover, 42 DElncRNAs were predicted as potential miRNA target mimics. LncRNAs have important effects on plant adaptation to drought conditions through the interaction with protein-encoding genes. The present study leads to greater insights into lncRNA biology and offers candidate regulators for improving the drought tolerance of sugar beet cultivars at the genetic level.
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spelling pubmed-99716292023-03-01 Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress Zou, Chunlei Guo, Zhiqiang Zhao, Shanshan Chen, Jishuai Zhang, Chunlai Han, Haoran Front Plant Sci Plant Science Drought stress is one of the most severe abiotic stresses that restrict global crop production. Long non-coding RNAs (lncRNAs) have been proved to play a key role in response to drought stress. However, genome-wide identification and characterization of drought-responsive lncRNAs in sugar beet is still lacking. Thus, the present study focused on analyzing lncRNAs in sugar beet under drought stress. We identified 32017 reliable lncRNAs in sugar beet by strand-specific high-throughput sequencing. A total of 386 differentially expressed lncRNAs (DElncRNAs) were found under drought stress. The most significantly upregulated and downregulated lncRNAs were TCONS_00055787 (upregulated by more than 6000 fold) and TCONS_00038334 (downregulated by more than 18000 fold), respectively. Quantitative real-time PCR results exhibited a high concordance with RNA sequencing data, which conformed that the expression patterns of lncRNAs based on RNA sequencing were highly reliable. In addition, we predicted 2353 and 9041 transcripts that were estimated to be the cis- and trans-target genes of the drought-responsive lncRNAs. As revealed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the target genes of DElncRNAs were significantly enriched in organelle subcompartment, thylakoid, endopeptidase activity, catalytic activity, developmental process, lipid metabolic process, RNA polymerase activity, transferase activity, flavonoid biosynthesis and several other terms associated with abiotic stress tolerance. Moreover, 42 DElncRNAs were predicted as potential miRNA target mimics. LncRNAs have important effects on plant adaptation to drought conditions through the interaction with protein-encoding genes. The present study leads to greater insights into lncRNA biology and offers candidate regulators for improving the drought tolerance of sugar beet cultivars at the genetic level. Frontiers Media S.A. 2023-02-14 /pmc/articles/PMC9971629/ /pubmed/36866366 http://dx.doi.org/10.3389/fpls.2023.1118011 Text en Copyright © 2023 Zou, Guo, Zhao, Chen, Zhang and Han https://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 Plant Science
Zou, Chunlei
Guo, Zhiqiang
Zhao, Shanshan
Chen, Jishuai
Zhang, Chunlai
Han, Haoran
Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress
title Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress
title_full Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress
title_fullStr Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress
title_full_unstemmed Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress
title_short Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress
title_sort genome-wide analysis of long non-coding rnas in sugar beet (beta vulgaris l.) under drought stress
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9971629/
https://www.ncbi.nlm.nih.gov/pubmed/36866366
http://dx.doi.org/10.3389/fpls.2023.1118011
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