Abstract
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.
Highlights
Several of the numerous RNAs that are transcribed by plant genomes, such as messenger RNAs, are translated into proteins
It seems that fruit development and Tomato yellow leaf curl virus (TYLCV) infection, which was included in our study, are two of the most important biological processes and pathogen responses associated with Long non-coding RNAs (lncRNAs) in tomato plants
The present study provides a comprehensive bioinformatics analysis of lncRNAs in tomato plants irradiated by neutrons, followed by TYLCV infection
Summary
Several of the numerous RNAs that are transcribed by plant genomes, such as messenger RNAs, are translated into proteins. LncRNAs have been identified in a limited number of plant species such as Arabidopsis thaliana, medicago, potato, rice, strawberry, tomato (Solanum lycopersicum), and maize (Guo & Liu, 2017; Kang et al, 2017; Nejat & Mantri, 2017; Scarano, Rao & Corrado, 2017; Zheng et al, 2017; Zhu et al, 2017). Studies revealing functional roles of identified lncRNAs in plants are rare. Previous studies using strand-specific RNAsequencing has identified several lncRNAs in Arabidopsis (Zhu et al, 2014) and banana (Li et al, 2017), which might be responsible to infection of Fusarium oxysporum. Another study has identified DROUGHT INDUCED lncRNA (DRIR) from Arabidopsis, which plays a role in responses of drought and salt stress (Qin et al, 2017)
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