title: Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis.
abstract: BACKGROUND
  The Emerald ash borer (EAB), Agrilus planipennis, is an invasive phloem-feeding insect pest of ash trees. Since its initial discovery near the Detroit, US- Windsor, Canada area in 2002, the spread of EAB has had strong negative economic, social and environmental impacts in both countries. Several transcriptomes from specific tissues including midgut, fat body and antenna have recently been generated. However, the relatively low sequence depth, gene coverage and completeness limited the usefulness of these EAB databases.
  
  
  RESULTS
  High-throughput deep RNA-Sequencing (RNA-Seq) was used to obtain 473.9 million pairs of 100 bp length paired-end reads from various life stages and tissues. These reads were assembled into 88,907 contigs using the Trinity strategy and integrated into 38,160 unigenes after redundant sequences were removed. We annotated 11,229 unigenes by searching against the public nr, Swiss-Prot and COG. The EAB transcriptome assembly was compared with 13 other sequenced insect species, resulting in the prediction of 536 unigenes that are Coleoptera-specific. Differential gene expression revealed that 290 unigenes are expressed during larval molting and 3,911 unigenes during metamorphosis from larvae to pupae, respectively (FDR< 0.01 and log2 FC>2). In addition, 1,167 differentially expressed unigenes were identified from larval and adult midguts, 435 unigenes were up-regulated in larval midgut and 732 unigenes were up-regulated in adult midgut. Most of the genes involved in RNA interference (RNAi) pathways were identified, which implies the existence of a system RNAi in EAB.
  
  
  CONCLUSIONS
  This study provides one of the most fundamental and comprehensive transcriptome resources available for EAB to date. Identification of the tissue- stage- or species- specific unigenes will benefit the further study of gene functions during growth and metamorphosis processes in EAB and other pest insects.
authors.affiliation: Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada; Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Jun
authors.initials: J
authors.lastname: Duan
authors.affiliation: Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada.
authors.forename: Tim
authors.initials: T
authors.lastname: Ladd
authors.affiliation: Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada.
authors.forename: Daniel
authors.initials: D
authors.lastname: Doucet
authors.affiliation: Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec City, Québec, Canada; Département de biochimie, de microbiologie et bio-informatique, Université Laval Québec City, Québec, Canada.
authors.forename: Michel
authors.initials: M
authors.lastname: Cusson
authors.affiliation: Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada.
authors.forename: Kees
authors.initials: K
authors.lastname: vanFrankenhuyzen
authors.affiliation: Department of Entomology, Ohio Agricultural and Research Development Center, The Ohio State University, Wooster, Ohio, United States of America.
authors.forename: Omprakash
authors.initials: O
authors.lastname: Mittapalli
authors.affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Krell
authors.affiliation: Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada.
authors.forename: Guoxing
authors.initials: G
authors.lastname: Quan
mesh_terms: D000818:Animals; D001517:Coleoptera / Q000235:genetics* / Q000254:growth & development; D030562:Databases, Protein; D031661:Fraxinus / Q000469:parasitology*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D059014:High-Throughput Nucleotide Sequencing; D019476:Insect Proteins / Q000235:genetics*; D008018:Life Cycle Stages; D058977:Molecular Sequence Annotation; D018978:Molting; D059467:Transcriptome
chemical_list: D019476:Insect Proteins