Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus

Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analy...

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Main Authors:	Yujie Zhou, Won Kyong Cho, Hee-Seong Byun, Vivek Chavan, Eui-Joon Kil, Sukchan Lee, Seung-Woo Hong
Format:	Article
Language:	English
Published:	PeerJ Inc. 2019-01-01
Series:	PeerJ
Subjects:	Next-generation sequencing Long non-coding RNA TYLCV infection Neutron irradiation RNA-Seq Tomato
Online Access:	https://peerj.com/articles/6286.pdf

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record_format	Article
spelling	doaj-01e0cb1994bd4edc8cd657c05037efed2020-11-25T01:49:07ZengPeerJ Inc.PeerJ2167-83592019-01-017e628610.7717/peerj.6286Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virusYujie Zhou0Won Kyong Cho1Hee-Seong Byun2Vivek Chavan3Eui-Joon Kil4Sukchan Lee5Seung-Woo Hong6Department of Energy Science, Sungkyunkwan University, Suwon, South KoreaResearch Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South KoreaDepartment of Integrative Biotechnology, Sungkyunkwan University, Suwon, South KoreaDepartment of Energy Science, Sungkyunkwan University, Suwon, South KoreaDepartment of Integrative Biotechnology, Sungkyunkwan University, Suwon, South KoreaDepartment of Integrative Biotechnology, Sungkyunkwan University, Suwon, South KoreaDepartment of Physics, Sungkyunkwan University, Suwon, South KoreaLong non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.https://peerj.com/articles/6286.pdfNext-generation sequencingLong non-coding RNATYLCV infectionNeutron irradiationRNA-SeqTomato
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Yujie Zhou Won Kyong Cho Hee-Seong Byun Vivek Chavan Eui-Joon Kil Sukchan Lee Seung-Woo Hong
spellingShingle	Yujie Zhou Won Kyong Cho Hee-Seong Byun Vivek Chavan Eui-Joon Kil Sukchan Lee Seung-Woo Hong Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus PeerJ Next-generation sequencing Long non-coding RNA TYLCV infection Neutron irradiation RNA-Seq Tomato
author_facet	Yujie Zhou Won Kyong Cho Hee-Seong Byun Vivek Chavan Eui-Joon Kil Sukchan Lee Seung-Woo Hong
author_sort	Yujie Zhou
title	Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus
title_short	Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus
title_full	Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus
title_fullStr	Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus
title_full_unstemmed	Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus
title_sort	genome-wide identification of long non-coding rnas in tomato plants irradiated by neutrons followed by infection with tomato yellow leaf curl virus
publisher	PeerJ Inc.
series	PeerJ
issn	2167-8359
publishDate	2019-01-01
description	Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.
topic	Next-generation sequencing Long non-coding RNA TYLCV infection Neutron irradiation RNA-Seq Tomato
url	https://peerj.com/articles/6286.pdf
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Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus

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