Identification and functional prediction of drought-responsive long non-coding RNA in tomato

Seung Hee Eom; Hee Ju Lee; Jin Hyoung Lee; Seung Hwan Wi; Sung Kyeom Kim; Tae Kyung Hyun

doi:10.3390/agronomy9100629

Identification and functional prediction of drought-responsive long non-coding RNA in tomato

Seung Hee Eom, Hee Ju Lee, Jin Hyoung Lee, Seung Hwan Wi, Sung Kyeom Kim, Tae Kyung Hyun

Department of Horticultural Science

Research output: Contribution to journal › Article › peer-review

29 Scopus citations

Abstract

In higher plants, several lines of evidence suggest that long non-coding RNAs (lncRNAs) may play important roles in the regulation of various biological processes by regulating gene expression. In this study, we identified a total of 521 lncRNAs, classified as intergenic, intronic, sense, and natural antisense lncRNAs, from RNA-seq data of drought-exposed tomato leaves. A further 244 drought-responsive tomato lncRNAs were predicted to be putative targets of 92 tomato miRNAs. Expression pattern and preliminary functional analysis of potentialmRNAtargets suggested that drought-responsive tomato lncRNAs play important roles in a variety of biological processes via lncRNA - mRNA co-expression. Taken together, these data present a comprehensive view of drought-responsive tomato lncRNAs that serve as a starting point for understanding the role of long intergenic non-coding RNAs in the regulatory mechanisms underlying drought responses in crops.

Original language	English
Article number	629
Journal	Agronomy
Volume	9
Issue number	10
DOIs	https://doi.org/10.3390/agronomy9100629
State	Published - 11 Oct 2019

Keywords

Drought
Long non-coding RNAs
miRNA
Tomato

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10.3390/agronomy9100629

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title = "Identification and functional prediction of drought-responsive long non-coding RNA in tomato",

abstract = "In higher plants, several lines of evidence suggest that long non-coding RNAs (lncRNAs) may play important roles in the regulation of various biological processes by regulating gene expression. In this study, we identified a total of 521 lncRNAs, classified as intergenic, intronic, sense, and natural antisense lncRNAs, from RNA-seq data of drought-exposed tomato leaves. A further 244 drought-responsive tomato lncRNAs were predicted to be putative targets of 92 tomato miRNAs. Expression pattern and preliminary functional analysis of potentialmRNAtargets suggested that drought-responsive tomato lncRNAs play important roles in a variety of biological processes via lncRNA - mRNA co-expression. Taken together, these data present a comprehensive view of drought-responsive tomato lncRNAs that serve as a starting point for understanding the role of long intergenic non-coding RNAs in the regulatory mechanisms underlying drought responses in crops.",

keywords = "Drought, Long non-coding RNAs, miRNA, Tomato",

author = "Eom, {Seung Hee} and Lee, {Hee Ju} and Lee, {Jin Hyoung} and Wi, {Seung Hwan} and Kim, {Sung Kyeom} and Hyun, {Tae Kyung}",

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T1 - Identification and functional prediction of drought-responsive long non-coding RNA in tomato

AU - Eom, Seung Hee

AU - Lee, Hee Ju

AU - Lee, Jin Hyoung

AU - Wi, Seung Hwan

AU - Kim, Sung Kyeom

AU - Hyun, Tae Kyung

PY - 2019/10/11

Y1 - 2019/10/11

N2 - In higher plants, several lines of evidence suggest that long non-coding RNAs (lncRNAs) may play important roles in the regulation of various biological processes by regulating gene expression. In this study, we identified a total of 521 lncRNAs, classified as intergenic, intronic, sense, and natural antisense lncRNAs, from RNA-seq data of drought-exposed tomato leaves. A further 244 drought-responsive tomato lncRNAs were predicted to be putative targets of 92 tomato miRNAs. Expression pattern and preliminary functional analysis of potentialmRNAtargets suggested that drought-responsive tomato lncRNAs play important roles in a variety of biological processes via lncRNA - mRNA co-expression. Taken together, these data present a comprehensive view of drought-responsive tomato lncRNAs that serve as a starting point for understanding the role of long intergenic non-coding RNAs in the regulatory mechanisms underlying drought responses in crops.

AB - In higher plants, several lines of evidence suggest that long non-coding RNAs (lncRNAs) may play important roles in the regulation of various biological processes by regulating gene expression. In this study, we identified a total of 521 lncRNAs, classified as intergenic, intronic, sense, and natural antisense lncRNAs, from RNA-seq data of drought-exposed tomato leaves. A further 244 drought-responsive tomato lncRNAs were predicted to be putative targets of 92 tomato miRNAs. Expression pattern and preliminary functional analysis of potentialmRNAtargets suggested that drought-responsive tomato lncRNAs play important roles in a variety of biological processes via lncRNA - mRNA co-expression. Taken together, these data present a comprehensive view of drought-responsive tomato lncRNAs that serve as a starting point for understanding the role of long intergenic non-coding RNAs in the regulatory mechanisms underlying drought responses in crops.

KW - Drought

KW - Long non-coding RNAs

KW - miRNA

KW - Tomato

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Identification and functional prediction of drought-responsive long non-coding RNA in tomato

Abstract

Keywords

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