Comparison of the Transcriptomes of Ginger (Zingiber officinale Rosc.) and Mango Ginger (Curcuma amada Roxb.) in Response to the Bacterial Wilt Infection

Abstract

Bacterial wilt in ginger (Zingiber officinale Rosc.) caused by Ralstonia solanacearum is one of the most important production constraints in tropical, sub-tropical and warm temperature regions of the world. Lack of resistant genotype adds constraints to the crop management. However, mango ginger (Curcuma amada Roxb.), which is resistant to R. solanacearum, is a potential donor, if the exact mechanism of resistance is understood. To identify genes involved in resistance to R. solanacearum, we have sequenced the transcriptome from wilt-sensitive ginger and wilt-resistant mango ginger using Illumina sequencing technology. A total of 26387032 and 22268804 paired-end reads were obtained after quality filtering for C. amada and Z. officinale, respectively. A total of 36359 and 32312 assembled transcript sequences were obtained from both the species. The functions of the unigenes cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. Large scale expression profiling showed that many of the disease resistance related genes were expressed more in C. amada. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either ginger or mango ginger. The identification of many defense related genes differentially expressed provides many insights to the resistance mechanism to R. solanacearum and for studying potential pathways involved in responses to pathogen. Also, several candidate genes that may underline the difference in resistance to R. solanacearum between ginger and mango ginger were identified. Finally, we have developed a web resource, ginger transcriptome database, which provides public access to the data. Our study is among the first to demonstrate the use of Illumina short read sequencing for de novo transcriptome assembly and comparison in non-model species of Zingiberaceae.

Whole Root Transcriptomic Analysis Reveals a Role for Auxin Pathways in Resistance toRalstonia solanacearumin Tomato

“…We observed a strong upregulation of terpene synthase genes specifically in roots of resistant plants. Analysis of ginger leaves after rhizome infection with R. solanacearum revealed a similar upregulation of terpene synthases in resistant plants (Prasath et al 2014). A previous report (Lin et al 2014) used virus-induced gene silencing in resistant H7996 to knock down expression of four TPS genes ( TPS31 , TPS32 , TPS33 , and TPS35 ) that were highly upregulated in our dataset.…”

De novo transcriptome analysis of halotolerant bacterium Staphylococcus sp. strain P-TSB-70 isolated from East coast of India: In search of salt stress tolerant genes

“…Differentially expressed transcripts recognized in control and treated conditions were analyzed through hierarchical clustering. The log-transformed and normalized value of transcripts was used to generate a heat map derived from Pearson correlation distance that is derived from the average linkage method [49,30].…”

Chitosan and oligochitosan enhance ginger (Zingiber officinale Roscoe) resistance to rhizome rot caused by Fusarium oxysporum in storage

“…Ginger, however, is subject to various fungal and bacterial pathogens that can cause diseases at different growth stages (Le, Smith, Hudler, & Aitken, 2014;Peng, Yuan, & Gao, 2013;Prasath et al, 2014;Shanmugam, Thakur et al, 2013). Among fungal pathogens, Fusarium oxysporum is especially a major problem in the production of ginger.…”