E-GEOD-9522 - HybridPoplar_H11-11_Leaves_MalacosomaDisstria_Herbivory

Status
Released on 22 April 2008, last updated on 2 May 2014
Organism
Populus trichocarpa x Populus deltoides
Samples (20)
Array (1)
Protocols (16)
Description
From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139 007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385 000 publicly available Populus ESTs. Clustering and assembly of 107 519 3'-end ESTs resulted in 14 451 contigs and 20 560 singletons, altogether representing 35 011 putative unique transcripts, or potentially more than three-quarters of the predicted c. 45 000 genes in the poplar genome. Using this EST resource, we developed a cDNA microarray containing 15 496 unique genes, which was utilized to monitor gene expression in poplar leaves in response to herbivory by forest tent caterpillars (Malacosoma disstria). After 24 h of feeding, 1191 genes were classified as up-regulated, compared to only 537 down-regulated. Functional classification of this induced gene set revealed genes with roles in plant defence (e.g. endochitinases, Kunitz protease inhibitors), octadecanoid and ethylene signalling (e.g. lipoxygenase, allene oxide synthase, 1-aminocyclopropane-1-carboxylate oxidase), transport (e.g. ABC proteins, calreticulin), secondary metabolism [e.g. polyphenol oxidase, isoflavone reductase, (–)-germacrene D synthase] and transcriptional regulation [e.g. leucine-rich repeat transmembrane kinase, several transcription factor classes (zinc finger C3H type, AP2/EREBP, WRKY, bHLH)]. This study provides the first genome-scale approach to characterize insect-induced defences in a woody perennial providing a solid platform for functional investigation of plant–insect interactions in poplar. Ten hybridizations were performed comparing FTC-treated poplar leaves after 24 h of continuous feeding and untreated control leaves harvested at the same time. RNA isolated from each of the five individual FTC-treated trees was compared directly against the five individual untreated control trees using two hybridizations with a dye flip for each tree pair.
Experiment type
unknown experiment type 
Contacts
Citation
Genomics of hybrid poplar (Populus trichocarpax deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences in poplar. Ralph S, Oddy C, Cooper D, Yueh H, Jancsik S, Kolosova N, Philippe RN, Aeschliman D, White R, Huber D, Ritland CE, Benoit F, Rigby T, Nantel A, Butterfield YS, Kirkpatrick R, Chun E, Liu J, Palmquist D, Wynhoven B, Stott J, Yang G, Barber S, Holt RA, Siddiqui A, Jones SJ, Marra MA, Ellis BE, Douglas CJ, Ritland K, Bohlmann J. , Europe PMC 16626454
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-9522.idf.txt
Sample and data relationshipE-GEOD-9522.sdrf.txt
Raw data (2)E-GEOD-9522.raw.1.zip, E-GEOD-9522.raw.2.zip
Processed data (1)E-GEOD-9522.processed.1.zip
Array designA-GEOD-5921.adf.txt
Links