title: 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.
abstract: As part of a genomics strategy to characterize inducible defences against insect herbivory in poplar, we developed a comprehensive suite of functional genomics resources including cDNA libraries, expressed sequence tags (ESTs) and a cDNA microarray platform. These resources are designed to complement the existing poplar genome sequence and poplar (Populus spp.) ESTs by focusing on herbivore- and elicitor-treated tissues and incorporating normalization methods to capture rare transcripts. 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.
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3.
authors.forename: Steven
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authors.lastname: Ralph
authors.forename: Claire
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authors.lastname: Oddy
authors.forename: Dawn
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authors.lastname: Cooper
authors.forename: Hesther
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authors.lastname: Yueh
authors.forename: Sharon
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authors.lastname: Jancsik
authors.forename: Natalia
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authors.lastname: Kolosova
authors.forename: Ryan N
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authors.forename: Dana
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authors.lastname: Aeschliman
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authors.forename: Dezene
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authors.lastname: Huber
authors.forename: Carol E
authors.initials: CE
authors.lastname: Ritland
authors.forename: François
authors.initials: F
authors.lastname: Benoit
authors.forename: Tracey
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authors.lastname: Rigby
authors.forename: André
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authors.lastname: Nantel
authors.forename: Yaron S N
authors.initials: YS
authors.lastname: Butterfield
authors.forename: Robert
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authors.lastname: Kirkpatrick
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authors.lastname: Chun
authors.forename: Jerry
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authors.lastname: Liu
authors.forename: Diana
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authors.lastname: Palmquist
authors.forename: Brian
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authors.lastname: Wynhoven
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authors.lastname: Stott
authors.forename: George
authors.initials: G
authors.lastname: Yang
authors.forename: Sarah
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authors.lastname: Barber
authors.forename: Robert A
authors.initials: RA
authors.lastname: Holt
authors.forename: Asim
authors.initials: A
authors.lastname: Siddiqui
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.forename: Marco A
authors.initials: MA
authors.lastname: Marra
authors.forename: Brian E
authors.initials: BE
authors.lastname: Ellis
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Douglas
authors.forename: Kermit
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authors.lastname: Ritland
authors.forename: Jörg
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authors.lastname: Bohlmann
mesh_terms: D000818:Animals; D018076:DNA, Complementary / Q000235:genetics; D004798:Enzymes / Q000235:genetics; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D015723:Gene Library; D005838:Genotype; D019476:Insect Proteins / Q000235:genetics; D007915:Lepidoptera / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010935:Plant Diseases / Q000382:microbiology; D032107:Populus / Q000235:genetics* / Q000378:metabolism / Q000382:microbiology; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary; D004798:Enzymes; D019476:Insect Proteins