利用高通量测序技术鉴定和分析香蕉根中早期枯萎病菌响应的 mRNAs 和长非编码 RNA。

Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing.

机构信息

Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China.

出版信息

Sci Rep. 2021 Aug 11;11(1):16363. doi: 10.1038/s41598-021-95832-8.

DOI:10.1038/s41598-021-95832-8

PMID:34381122

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8358008/

Abstract

Fusarium wilt disease, caused by Fusarium oxysporum f.sp. cubense (Foc), has been recognized as the most devastating disease to banana. The regulatory role of long non-coding RNAs (lncRNAs) in plant defense has been verified in many plant species. However, the understanding of their role during early FocTR4 (Foc tropical race 4) infection stage is very limited. In this study, lncRNA sequencing was used to reveal banana root transcriptome profile changes during early FocTR4 infection stages. Quantitative real time PCR (qRT-PCR) was performed to confirm the expression of eight differentially expressed (DE) lncRNAs (DELs) and their predicted target genes (DETs), and three DE genes (DEGs). Totally, 12,109 lncRNAs, 36,519 mRNAs and 2642 novel genes were obtained, of which 1398 (including 78 DELs, 1220 DE known genes and 100 DE novel genes) were identified as FocTR4 responsive DE transcripts. Gene function analysis revealed that most DEGs were involved in biosynthesis of secondary metabolites, plant-pathogen interaction, plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis, alpha-linolenic acid metabolism and so on. Coincidently, many DETs have been identified as DEGs in previous transcriptome studies. Moreover, many DETs were found to be involved in ribosome, oxidative phosphorylation, lipoic acid metabolism, ubiquitin mediated proteolysis, N-glycan biosynthesis, protein processing in endoplasmic reticulum and DNA damage response pathways. QRT-PCR result showed the expression patterns of the selected transcripts were mostly consistent with our lncRNA sequencing data. Our present study showed the regulatory role of lncRNAs on known biotic and abiotic stress responsive genes and some new-found FocTR4 responsive genes, which can provide new insights into FocTR4-induced changes in the banana root transcriptome during the early pathogen infection stage.

摘要

枯萎病，由尖孢镰刀菌古巴专化型（Foc）引起，被认为是对香蕉最具破坏性的疾病。长链非编码 RNA（lncRNAs）在植物防御中的调节作用已在许多植物物种中得到验证。然而，在早期 FocTR4（Foc 热带种 4）感染阶段，对它们的作用的了解非常有限。在这项研究中，使用 lncRNA 测序来揭示香蕉根在早期 FocTR4 感染阶段转录组谱的变化。进行定量实时 PCR（qRT-PCR）以验证八个差异表达（DE）lncRNA（DEL）及其预测靶基因（DET）和三个 DE 基因（DEG）的表达。总共获得了 12109 个 lncRNA、36519 个 mRNA 和 2642 个新基因，其中 1398 个（包括 78 个 DEL、1220 个已知的 DEG 和 100 个新的 DEG）被鉴定为 FocTR4 响应的 DE 转录物。基因功能分析表明，大多数 DEG 参与次生代谢物的生物合成、植物-病原体相互作用、植物激素信号转导、苯丙氨酸代谢、苯丙烷生物合成、α-亚麻酸代谢等。巧合的是，许多 DET 已被鉴定为先前转录组研究中的 DEG。此外，许多 DET 被发现参与核糖体、氧化磷酸化、硫辛酸代谢、泛素介导的蛋白水解、N-聚糖生物合成、内质网蛋白加工和 DNA 损伤反应途径。qRT-PCR 结果表明，所选转录本的表达模式与我们的 lncRNA 测序数据大多一致。本研究表明，lncRNA 对已知生物和非生物胁迫响应基因以及一些新发现的 FocTR4 响应基因的调节作用，为香蕉根在早期病原菌感染阶段转录组因 FocTR4 诱导而发生变化提供了新的见解。