Transcriptomic analysis to reveal the differentially expressed miRNA targets and their miRNAs in response to Ralstonia solanacearum in ginger species

Mohandas Snigdha,Duraisamy Prasath

doi:10.1186/s12870-021-03108-0

Abstract

BackgroundBacterial wilt is the most devastating disease in ginger caused by Ralstonia solanacearum. Even though ginger (Zingiber officinale) and mango ginger (Curcuma amada) are from the same family Zingiberaceae, the latter is resistant to R. solanacearum infection. MicroRNAs have been identified in many crops which regulates plant-pathogen interaction, either through silencing genes or by blocking mRNA translation. However, miRNA’s vital role and its targets in mango ginger in protecting bacterial wilt is not yet studied extensively. In the present study, using the “psRNATarget” server, we analyzed available ginger (susceptible) and mango ginger (resistant) transcriptome to delineate and compare the microRNAs (miRNA) and their target genes (miRTGs).ResultsA total of 4736 and 4485 differential expressed miRTGs (DEmiRTGs) were identified in ginger and mango ginger, respectively, in response to R. solanacearum. Functional annotation results showed that mango ginger had higher enrichment than ginger in top enriched GO terms. Among the DEmiRTGs, 2105 were common in ginger and mango ginger. However, 2337 miRTGs were expressed only in mango ginger which includes 62 defence related and upregulated miRTGs. We also identified 213 miRTGs upregulated in mango ginger but downregulated in ginger, out of which 23 DEmiRTGS were defence response related. We selected nine miRNA/miRTGs pairs from the data set of common miRTGs of ginger and mango ginger and validated using qPCR.ConclusionsOur data covered the expression information of 9221 miRTGs. We identified nine miRNA/miRTGs key candidate pairs in response to R. solanacearum infection in ginger. This is the first report of the integrated analysis of miRTGs and miRNAs in response to R. solanacearum infection among ginger species. This study is expected to deliver several insights in understanding the miRNA regulatory network in ginger and mango ginger response to bacterial wilt.

Highlights

Bacterial wilt is the most devastating disease in ginger caused by Ralstonia solanacearum
Our results provided valuable information to reveal the molecular mechanism of miRNAs and their targets in resisting mango ginger against R. solanacearum infection
The mango ginger assembly was represented by 307,952 contigs with an average of 845.32 bps, while the ginger assembly was represented by 303,878 contigs with an average contig size of 692.32 bps

Summary

Introduction

Bacterial wilt is the most devastating disease in ginger caused by Ralstonia solanacearum. Even though ginger (Zingiber officinale) and mango ginger (Curcuma amada) are from the same family Zingiberaceae, the latter is resistant to R. solanacearum infection. The R. solanacearum, a soil-borne bacterium, causes bacterial wilt in many plant families such as tomato, potato, pepper, peanut, banana and eggplant [6]. This gram-negative bacterium infects plants through axils of secondary roots, which later invades cortex and colonizes in the xylem vessels which causes wilt symptoms and death [7]. The ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, reported mango ginger (Curcuma amada Roxb.) from the ginger family Zingiberaceae, with a high level of resistance against bacterial wilt. Comparative transcriptomics of ginger and mango ginger during bacterial wilt has resulted in identifying a considerable number of candidate genes [10]

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Results

Discussion

Conclusion