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

Abstract

Background 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. 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). Results A 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. Conclusions Our 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.

Induced defense strategies of plants against Ralstonia solanacearum

“…solanacearum infestation ( Hwang et al, 2011 ). Other plants such as Arabidopsis ( Zhao et al, 2019 ), tomato ( French et al, 2018 ), potato ( Zuluaga et al, 2015 ), ginger ( Snigdha and Prasath, 2021 ), and aubergine ( Chen et al, 2018 ) showed a similar situation after inoculation with R . solanacearum .…”

“…In pepper, genes associated with xylan biosynthesis and cell wall organization were significantly enriched in response to R. solanacearum infestation (Hwang et al, 2011). Other plants such as Arabidopsis (Zhao et al, 2019), tomato (French et al, 2018), potato (Zuluaga et al, 2015), ginger (Snigdha and Prasath, 2021), and aubergine (Chen et al, 2018) showed a similar situation after inoculation with R. solanacearum. All of this evidence suggests a role for the cell wall in defense against R. solanacearum infestation.…”

Genome-Wide Characterization and Expression Analysis of Transcription Factor Families in Desert Moss Syntrichia caninervis under Abiotic Stresses

“…In the model plants, microRNA159 ( Ath - miR159 a,b,c) is a highly preserved miRNA in plants and contributes to stress responses [ 63 ]. Ath- miR5658 , Ath - miR858 , and Ath - miR1886 were also found to be responses to various stress tolerances [ 64 , 65 , 66 ]. In this work, we identified several miRNAs from Arabidopsis and P. patens that theoretically target overrepresented TF families in S. caninervis , similar to previous report s , stress-related miRNAs also target many TFs in S. caninervis , such as Ath-miR5658 potentially targeted four ScTF s members (Sc_ g03411_bHLH , Sc_g06422_ERF , and Sc_g02274_MYB ) and Ath-miR159 can specifically target Sc _ g13935_MYB.…”

A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges

“…lncRNA expression is cell-type- or tissue-specific, developmentally regulated, and may differ in response to numerous stimuli ( Derrien et al, 2012 ). miRNAs are a new class of small, non-coding RNAs (20–24 nucleotides in length) that regulate gene expression at the post-transcriptional level through mRNA cleavage or translational inhibition ( Snigdha and Prasath, 2021 ; Chandra et al, 2023 ). In recent years, the identification and functional analysis of plant miRNAs has become one of the hottest research areas in plant science due to their role in almost all biological and metabolic processes, including plant organ development, signaling pathways, disease, and stress responses ( Sun et al, 2012 ; Anjali et al, 2017 ; Chandra et al, 2023 ).…”