Poster: Molecular & Cellular Plant-Microbe Interactions: MPMI
Devising a custom 13K unigene-based Nicotiana benthamiana microarray to study host-pathogen interactions at the transcriptome level
P. THAMMARAT (1), P. Thammarat (1), T. Sit (2), S. Lommel (2) (1) Functional Genomics Program, North Carolina State University, U.S.A.; (2) Department of Entomology and Plant Pathology, North Carolina State University, U.S.A.
Selecting a model plant to study host/pathogen interactions at the transcriptome level is a crucial part of experimental design. Although Arabidopsis thaliana is a preferred model based on the availability of comprehensive genomic information, it is only susceptible to a restricted number of pathogens. Due to this limitation, exploring alternative plant models is necessary. Nicotiana benthamiana (Nb) is highly susceptible to a wide range of pathogens. In order to enable the use of Nb in high-throughput studies, we created a genomic tool for this plant. We developed the first Nb array from 13,014 unigenes (average 752 bp) which were originally derived from 40,000 expressed sequence tags (ESTs; ~70% of publicly available Nb ESTs representing ~38% of the transcriptome). Homology searches against GenBank, KEGG, and GO databases (BLASTX, E-value < 1x10-5) indicated that 66% of the unigenes have > one hit, with the most frequent hit to Solanaceae plants. Our unigene-based array has broad coverage of plant pathways: metabolism, transportation, transcription, translation, signal transduction and defense. 261 unigenes were involved in transcription with the most abundant ones belonging to the AP2/ERF, WRKY and GRAS families. The Nb array consists of 9 probes per unigene. We conducted an array performance test to study interactions between Nb and Red clover necrotic mosaic virus. The array successfully yielded 100% hybridization capacity to Nb mock and infected samples.