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

Raphael Anue Mensah,Fan Liu,Jiapeng Liu,Junwei Wu,Dan Li,Xueli Sun,Na Tian,Bin Wang,Chunzhen Cheng,Zhongxiong Lai

doi:10.1038/s41598-021-95832-8

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.

Highlights

Abbreviations Foc tropical race 4 (FocTR4) Fusarium oxysporum F. sp. cubense Tropical Race 4 FW Fusarium wilt long non-coding RNAs (lncRNAs) Long noncoding RNA differentially expressed (DE) genes (DEGs) Differentially expressed gene DEL Differentially expressed lncRNA DELs and their target genes (DETs) Target gene of DEL bp Base pair ethylene-responsive transcription factors (ERFs) Ethylene-responsive transcription factor DOPA2 Tyrosine/DOPA decarboxylase 2 LHCB Light harvesting chlorophyll a–b binding protein TUBB7 Tubulin beta-7 chain like gene
The expression diversity of lncRNAs was higher than mRNA, while their expression frequency was significantly lower than mRNA (Fig. 1), which was consistent with the result in Miscanthus lutarioriparius[53]
The least amounts of lncRNAs were identified in chromosome 2, which is the shortest chromosome of banana (Fig. 2)

Summary

Introduction

Abbreviations FocTR4 Fusarium oxysporum F. sp. cubense Tropical Race 4 FW Fusarium wilt lncRNA Long noncoding RNA DEG Differentially expressed gene DEL Differentially expressed lncRNA DETs Target gene of DEL bp Base pair ERF Ethylene-responsive transcription factor DOPA2 Tyrosine/DOPA decarboxylase 2 LHCB Light harvesting chlorophyll a–b binding protein TUBB7 Tubulin beta-7 chain like gene. High throughput sequencing method has been applied by scientists to compare the mRNA changes of one banana variety at different infection time points after Foc 1 or FocTR4 infection[11,12] or both[13], and two banana varieties (one is tolerant to FocTR4 and the other is susceptible) to FocTR4 infection[10] for the exploration of candidate FW resistant genes. These transcriptomic analysis provided insights into the molecular mechanism associated with banana-Foc interaction, and genes involved in phenylalanine metabolism, phenylpropanoid biosynthesis, alpha-linolenic acid metabolism, phytohormone biosynthesis and signaling, cell wall lignification and so on were identified to contribute to the FW resistance of banana. The target genes of these DELs were mainly involved in lignin biosynthesis, plant pathogen interaction and plant hormone signaling and so on, suggesting that lncRNA play important role in Paulownia–phytoplasmas interaction, at least partially, by regulating the plant defense p athways[65]

Methods

Results

Discussion

Conclusion