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Identification and functional prediction of salt stress-related long noncoding RNAs in grapevine roots
Environmental and Experimental Botany ( IF 4.5 ) Pub Date : 2020-11-01 , DOI: 10.1016/j.envexpbot.2020.104215 Zhongxin Jin , Shiwei Gao , Wanyun Ma , Xinning Lyu , Xiaolei Cao , Yuxin Yao
Environmental and Experimental Botany ( IF 4.5 ) Pub Date : 2020-11-01 , DOI: 10.1016/j.envexpbot.2020.104215 Zhongxin Jin , Shiwei Gao , Wanyun Ma , Xinning Lyu , Xiaolei Cao , Yuxin Yao
Abstract Long noncoding RNAs (lncRNAs) are a widespread RNA molecules of more than 200 bp that lack coding potential and have been proven to function in response to abiotic stresses. In this study, we identified salt stress-induced lncRNAs in grapevine roots and predicted their intricate regulatory roles. A total of 3952 novel lncRNAs that were distributed across all 19 grape chromosomes, more than 70 % of which were located in intergenic regions. Compared with mRNAs, lncRNAs exhibit short ORFs, a high SNP density and low expression. A total of 1661 differentially expressed lncRNAs (DElncRNAs) were detected in salt-treated roots in comparison to the control, and the greatest number of DElncRNAs were produced in the roots at 12 h after salt treatment. We predicted that 546, 771, and 608 mRNAs could be directly or indirectly regulated by DElncRNAs in cis-, trans-, and miRNA-mediated patterns. Multiple target genes of DElncRNAs were found to be involved in transcriptional regulation, the ubiquitin-proteasome pathway, multiple ion binding, and electron carrier activity. Furthermore, a large number of NB-ARC domain proteins are potential targets of DElncRNAs. These findings provide a comprehensive view of potentially functional lncRNAs, providing insight into the molecular mechanism of salt resistance in grape.
更新日期：2020-11-01
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