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

Sex and molecular differences in cardiovascular parameters at peak influenza disease in mice.

There is a growing interest in the detection of subtle changes in cardiovascular physiology in response to viral infection to develop better disease surveillance strategies. This is not only important for earlier diagnosis and better prognosis of symptomatic carriers but also useful to diagnose asymptomatic carriers of the virus. Previous studies provide strong evidence of an association between inflammatory biomarker levels and both blood pressure (BP) and heart rate (HR) during infection. The identification of novel biomarkers during an inflammatory event could significantly improve predictions for cardiovascular events. Thus, we evaluated changes in cardiovascular physiology induced in A/Puerto Rico/8/34 (PR8) influenza infections in female and male C57BL/6J mice and compared them with the traditional method of influenza disease detection using body weight (BW). Using radiotelemetry, changes in BP, HR, and activity were studied. Change in BW of infected females was significantly decreased from 5 to 13 days postinfection (dpi), yet alterations in normal physiology including loss of diurnal rhythm and reduced activity was observed starting at about 3 dpi for HR and 4 dpi for activity and BP; continuing until about 13 dpi. In contrast, males had significantly decreased BW 8 to 12 dpi and demonstrated altered physiological measurements for a shorter period compared with females with a reduction starting at 5 dpi for activity, 6 dpi for BP, and 7 dpi for HR until about 12 dpi, 10 dpi, and 9 dpi, respectively. Finally, females and males exhibited different patterns of inflammatory maker expression in lungs at peak disease by analyzing bulk RNA-sequencing data for lungs and Bio-plex cytokine assay for blood collected from influenza-infected and naïve C57BL/6J female and male mice at 7 dpi. In total, this study provides insight into cardiovascular changes and molecular markers to distinguish sex differences in peak disease caused by influenza virus infection

Phylogenetic relationships of polygalacturonase transcripts of <i>L</i>. <i>lineolaris</i> with polygalacturonases from other mirid bugs.

<p>Phylogenetic relationships of polygalacturonase transcripts of <i>L</i>. <i>lineolaris</i> with polygalacturonases from other mirid bugs.</p

Insight into the Salivary Gland Transcriptome of <i>Lygus lineolaris</i> (Palisot de Beauvois)

<div><p>The tarnished plant bug (TPB), <i>Lygus lineolaris</i> (Palisot de Beauvois) is a polyphagous, phytophagous insect that has emerged as a major pest of cotton, alfalfa, fruits, and vegetable crops in the eastern United States and Canada. Using its piercing-sucking mouthparts, TPB employs a “lacerate and flush” feeding strategy in which saliva injected into plant tissue degrades cell wall components and lyses cells whose contents are subsequently imbibed by the TPB. It is known that a major component of TPB saliva is the polygalacturonase enzymes that degrade the pectin in the cell walls. However, not much is known about the other components of the saliva of this important pest. In this study, we explored the salivary gland transcriptome of TPB using Illumina sequencing. After <i>in silico</i> conversion of RNA sequences into corresponding polypeptides, 25,767 putative proteins were discovered. Of these, 19,540 (78.83%) showed significant similarity to known proteins in the either the NCBI nr or Uniprot databases. Gene ontology (GO) terms were assigned to 7,512 proteins, and 791 proteins in the sialotranscriptome of TPB were found to collectively map to 107 Kyoto Encyclopedia of Genes and Genomes (KEGG) database pathways. A total of 3,653 Pfam domains were identified in 10,421 sialotranscriptome predicted proteins resulting in 12,814 Pfam annotations; some proteins had more than one Pfam domain. Functional annotation revealed a number of salivary gland proteins that potentially facilitate degradation of host plant tissues and mitigation of the host plant defense response. These transcripts/proteins and their potential roles in TPB establishment are described.</p></div

Scanning electron micrograph of excised salivary glands of the tarnished plant bug <i>Lygus lineolaris</i>.

<p>Scanning electron micrograph of excised salivary glands of the tarnished plant bug <i>Lygus lineolaris</i>.</p

Venn diagram showing distribution of 15,980 <i>L</i>. <i>lineolaris</i> salivary gland proteins with BLASTP alignments to <i>Acyrthosiphon pisum</i>, <i>Drosophila melanogaster</i>, <i>Tribolium castaneum</i>, and <i>Lygus hesperus</i>.

<p>Venn diagram showing distribution of 15,980 <i>L</i>. <i>lineolaris</i> salivary gland proteins with BLASTP alignments to <i>Acyrthosiphon pisum</i>, <i>Drosophila melanogaster</i>, <i>Tribolium castaneum</i>, and <i>Lygus hesperus</i>.</p