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Transcriptomic analysis of ncRNAs and mRNAs interactions during drought stress in switchgrass

文献类型： 外文期刊

作者： Guan, Cong 1 ; Li, Wei 1 ; Wang, Guoliang 1 ; Yang, Ruimei 1 ; Zhang, Jinglei 1 ; Zhang, Jinhong 1 ; Wu, Bo 1 ; Gao, Run 1 ; Jia, Chunlin 1 ;

作者机构： 1.Shandong Acad Agr Sci, Inst Leisure Agr, Jinan 250100, Peoples R China

2.Minist Agr, Key Lab East China Urban Agr, Jinan 250100, Peoples R China

3.Shandong Engn Res Ctr Ecol l & Hort Plant Breeding, Jinan 250100, Peoples R China

4.China Agr Univ, Coll Grassland Sci & Technol, 2 Yuan Mingyuan West Rd, Beijing 100193, Peoples R China

关键词： Switchgrass; Starch and sucrose metabolism pathway; Starch synthase 4 (PvSS4); Novel_miRNA122; Novel_miRNA14; Drought stress; CeRNA networks

期刊名称：PLANT SCIENCE （ 影响因子：5.2； 五年影响因子：5.7 ）

ISSN： 0168-9452

年卷期： 2024 年 339 卷

页码：

收录情况： SCI

摘要： Switchgrass (Panicum virgatum L.) plays a pivotal role as a bioenergy feedstock in the production of cellulosic ethanol and contributes significantly to enhancing ecological grasslands and soil quality. The utilization of noncoding RNAs (ncRNAs) has gained momentum in deciphering the intricate genetic responses to abiotic stress in various plant species. Nevertheless, the current research landscape lacks a comprehensive exploration of the responses of diverse ncRNAs, including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), to drought stress in switchgrass. In this study, we employed whole transcriptome sequencing to comprehensively characterize the expression profiles of both mRNA and ncRNAs during episodes of drought stress in switchgrass. Our analysis identified a total of 12,511 mRNAs, 59 miRNAs, 38 circRNAs, and 368 lncRNAs that exhibited significant differential expression between normal and drought-treated switchgrass leaves. Notably, the majority of up-regulated mRNAs displayed pronounced enrichment within the starch and sucrose metabolism pathway, as validated through KEGG analysis. Co-expression analysis illuminated that differentially expressed (DE) lncRNAs conceivably regulated 1308 protein-coding genes in trans and 7110 protein-coding genes in cis. Furthermore, both cis- and trans-target mRNAs of DE lncRNAs exhibited enrichment in four common KEGG pathways. The intricate interplay between lncRNAs and circRNAs with miRNAs via miRNA response elements was explored within the competitive endogenous RNA (ceRNA) network framework. As a result, we constructed elaborate regulatory networks, including lncRNA-novel_miRNA480-mRNA, lncRNAnovel_miRNA304-mRNA, lncRNA/circRNA-novel_miRNA122-PvSS4, and lncRNA/circRNA-novel_miRNA14PvSS4, and subsequently validated the functionality of the target gene, starch synthase 4 (PvSS4). Furthermore, through the overexpression of PvSS4, we ascertained its capacity to enhance drought tolerance in yeast. However, it is noteworthy that PvSS4 did not exhibit any discernible impact under salt stress conditions. These findings, as presented herein, not only contribute substantively to our understanding of ceRNA networks but also offer a basis for further investigations into their potential functions in response to drought stress in switchgrass.

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