Discovery, identification, and functional characterization of long noncoding RNAs inArachis hypogaeaL.

文献类型： 外文期刊

第一作者： Tian, Haiying

作者： Tian, Haiying;Li, Xinguo;Peng, Zhenying;Wan, Shubo;Guo, Feng;Meng, Jingjing;Li, Xinguo;Peng, Zhenying;Zhang, Zhimeng;Ding, Hong;Wan, Shubo

作者机构：

关键词： Arachis hypogaeaL; Transcriptome analysis; lncRNAs; Alternative splicing; Organ-specific expression; Salt-stress

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2020 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Background Long noncoding RNAs (lncRNAs), which are typically > 200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaeaL.) largely remain unknown. Results A genome-wide scan of the peanut (Arachis hypogaeaL.) transcriptome identified 1442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. Approximately 44.17% of the lncRNAs with an exon/intron structure were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. Conclusions This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.

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[1]Discovery, identification, and functional characterization of long noncoding RNAs inArachis hypogaeaL.. Tian, Haiying,Li, Xinguo,Peng, Zhenying,Wan, Shubo,Guo, Feng,Meng, Jingjing,Li, Xinguo,Peng, Zhenying,Zhang, Zhimeng,Ding, Hong,Wan, Shubo. 2020

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