Transcriptomic dissection of the rice – Burkholderia glumae interaction

BACKGROUND: Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistance. To understand the interaction between rice and Burkholderia glumae, we used transcriptomics via next-generation sequencing (RNA-Seq) and bioinformatics to identify differentially expressed transcripts between resistant and susceptible interactions and formulate a model for rice resistance to the disease. RESULTS: Using inoculated young seedlings as sample tissues, we identified unique transcripts involved with resistance to bacterial panicle blight, including a PIF-like ORF1 and verified differential expression of some selected genes using qRT-PCR. These transcripts, which include resistance genes of the NBS-LRR type, kinases, transcription factors, transporters and expressed proteins with functions that are not known, have not been reported in other pathosystems including rice blast or bacterial blight. Further, functional annotation analysis reveals enrichment of defense response and programmed cell death (biological processes); ATP and protein binding (molecular functions); and mitochondrion-related (cell component) transcripts in the resistant interaction. CONCLUSION: Taken together, we formulated a model for rice resistance to bacterial panicle blight that involves an activation of previously unknown resistance genes and their activation partners upon challenge with B. glumae. Other interesting findings are that 1) though these resistance transcripts were up-regulated upon inoculation in the resistant interaction, some of them were already expressed in the water-inoculated control from the resistant genotype, but not in the water- and bacterium-inoculated samples from the susceptible genotype; 2) rice may have co-opted an ORF that was previously a part of a transposable element to aid in the resistance mechanism; and 3) resistance may have existed immediately prior to rice domestication. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-755) contains supplementary material, which is available to authorized users

A genomic resource for the sedentary semi-endoparasitic reniform nematode, Rotylenchulus reniformis Linford & Oliveira.

The reniform nematode (Rotylenchulus reniformis) is a sedentary semi-endoparasitic species that is pathogenic on many row crops, fruits, and vegetables. Here, the authors present a draft genome assembly of R. reniformis using small- and large-insert libraries sequenced on the Illumina GAIIx and MiSeq platforms. The reniform nematode (Rotylenchulus reniformis) is a sedentary semi-endoparasitic species that is pathogenic on many row crops, fruits, and vegetables. Here, the authors present a draft genome assembly of R. reniformis using small- and large-insert libraries sequenced on the Illumina GAIIx and MiSeq platforms

Quantitative field testing Rotylenchulus reniformis DNA from metagenomic samples isolated directly from soil.

A quantitative PCR procedure targeting the ?-tubulin gene determined the number of Rotylenchulus reniformis Linford & Oliveira 1940 in metagenomic DNA samples isolated from soil. Of note, this outcome was in the presence of other soil-dwelling plant parasitic nematodes including its sister genus Helicotylenchus Steiner, 1945. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from soil

Number of nematodes per 500 cm³ of soil used in field assay.

<p>Number of nematodes per 500 cm³ of soil used in field assay.</p

Amplification characteristics of the Rr-β-TUB qPCR primers under standard PCR conditions on metagenomic DNA isolated directly from soil collected at the South Farm (SF) and cotton (Ct) sites.

<p>The number of nematodes whose DNA was isolated is provided below the amplicon in each reaction. Rr-β-TUB primed reactions. Lane 1, SF1; Lane 2, SF2; Lane 3, Ct1 sample 1; Lane 4, Ct2 sample 2; Lane 5, Ct3 sample 3; Lane 6, No DNA; Lane 7, No Primers.</p

Specificity of the Rr- β-TUB qPCR primers under standard PCR conditions from known numbers of <i>R. reniformis</i>.

<p><i>R. reniformis</i> DNA was isolated from vermiform J2s serving as the template. The Rr-β-TUB-primed reactions. Abbreviation, R.r. - <i>R. reniformis</i>. Lane 1, 1000 R.r.; Lane 2, 1000 R.r.; Lane 3, 1000 R.r.; Lane 4, 100 R.r.; Lane 5, 100 R.r.; Lane 6, 100 R.r.; Lane 7, 10 R.r.; Lane 8, 10 R.r.; Lane 9, 10 R.r.; Lane 10, 1 R.r.; Lane 11, 1 R.r.; Lane 12, 1 R.r.; Lane 13, 1 R.r.; Lane 14, No DNA; Lane 15, No primers.</p

<i>R. reniformis</i> β-tub primers for qPCR assay.

<p><i>R. reniformis</i> β-tub primers for qPCR assay.</p