Distribution of similarity search results showed by Venn diagrams.

<p>The number of unique sequence-based annotations is the sum of unique best BLASTX hits from the GO term, Pfam domains and KEGG databases, respectively. The overlap regions among the three circles contain the number of unigenes that share BLASTX similarity with respective databases.</p

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

<div><p>Bacterial wilt in ginger (<i>Zingiber officinale</i> Rosc.) caused by <i>Ralstonia solanacearum</i> 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 (<i>Curcuma amada</i> Roxb.), which is resistant to <i>R. solanacearum</i>, is a potential donor, if the exact mechanism of resistance is understood. To identify genes involved in resistance to <i>R. solanacearum</i>, 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 <i>C. amada</i> and <i>Z. officinale</i>, 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 <i>C. amada</i>. 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 <i>R. solanacearum</i> and for studying potential pathways involved in responses to pathogen. Also, several candidate genes that may underline the difference in resistance to <i>R. solanacearum</i> 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 <i>de novo</i> transcriptome assembly and comparison in non-model species of Zingiberaceae.</p></div

List of upregulated isoprene/terpene biosynthesis genes in <i>C. amada.</i>

<p>List of upregulated isoprene/terpene biosynthesis genes in <i>C. amada.</i></p

Summary of transcription factor unigenes of <i>C. amada</i> and <i>Z. officinale.</i>

<p>Summary of transcription factor unigenes of <i>C. amada</i> and <i>Z. officinale.</i></p

Divergence in the expression levels of transcription factors (TF) transcripts between C. amada and Z. officinale.

<p>Heat map and clustering analysis of the transcripts of genes encoding TFs are shown. Higher expression of TFs occurs in <i>C. amada</i>. The high expression levels are depicted in purple and low expression in red. Clustering and heat map was drawn with CLC Genomics Workbench based on an Euclidean distance matrix, after normalization of expression values.</p

Assembly summary of <i>C. amada</i> and <i>Z. officinale.</i>

<p>Assembly summary of <i>C. amada</i> and <i>Z. officinale.</i></p

Summary of genes with high expression levels in response to <i>R. solanacearum</i> in <i>C. amada,</i> listed according to function.

<p>*Fold-change between <i>C. amada</i> and <i>Z. officinale</i>, using fold-regulation cutoff of >3.0, <i>P</i><0.005, FDR <i>P</i> at 0.05%.</p

Histogram showing the significantly enriched Gene Ontology terms associated with up regulated genes in <i>C. amada</i>.

<p>The y-axis indicates the number of genes in a category.</p

Pearson’s correlation coefficient between <i>C. amada</i> and <i>Z. officinale</i> transcriptomes.

<p>Comparisons of estimated RPKM distributions between <i>C. amada</i> and <i>Z. officinale</i> and <i>R. solanacearum</i> interactions. Pearson’s correlation coefficients (<i>R</i>²) between transcriptomes are presented.</p

Sequence length distribution of assembled contigs in the transcriptomes of C. amada and Z. officinale.

<p>Histogram presentation of sequence-length distribution for significant matches that was found. The x-axis indicates sequence sizes from 300 nt to >10001 nt. The y-axis indicates the number of contigs for every given size range.</p