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

PeerJ

article

Yujie Zhou¹  Won Kyong Cho²  Hee-Seong Byun³  Vivek Chavan¹  Eui-Joon Kil³  Sukchan Lee³  Seung-Woo Hong⁴ 

[1] Department of Energy Science, Sungkyunkwan University;Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University;Department of Integrative Biotechnology, Sungkyunkwan University;Department of Physics, Sungkyunkwan University

关键词: Next-generation sequencing;    Long non-coding RNA;    TYLCV infection;    Neutron irradiation;    RNA-Seq;    Tomato;   

DOI  :  10.7717/peerj.6286

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY