title: KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella.
abstract: BACKGROUND
  The diamondback moth (DBM), Plutella xylostella, is one of the most harmful insect pests for crucifer crops worldwide. DBM has rapidly evolved high resistance to most conventional insecticides such as pyrethroids, organophosphates, fipronil, spinosad, Bacillus thuringiensis, and diamides. Therefore, it is important to develop genomic and transcriptomic DBM resources for analysis of genes related to insecticide resistance, both to clarify the mechanism of resistance of DBM and to facilitate the development of insecticides with a novel mode of action for more effective and environmentally less harmful insecticide rotation. To contribute to this goal, we developed KONAGAbase, a genomic and transcriptomic database for DBM (KONAGA is the Japanese word for DBM).
  
  
  METHODS
  KONAGAbase provides (1) transcriptomic sequences of 37,340 ESTs/mRNAs and 147,370 RNA-seq contigs which were clustered and assembled into 84,570 unigenes (30,695 contigs, 50,548 pseudo singletons, and 3,327 singletons); and (2) genomic sequences of 88,530 WGS contigs with 246,244 degenerate contigs and 106,455 singletons from which 6,310 de novo identified repeat sequences and 34,890 predicted gene-coding sequences were extracted. The unigenes and predicted gene-coding sequences were clustered and 32,800 representative sequences were extracted as a comprehensive putative gene set. These sequences were annotated with BLAST descriptions, Gene Ontology (GO) terms, and Pfam descriptions, respectively. KONAGAbase contains rich graphical user interface (GUI)-based web interfaces for easy and efficient searching, browsing, and downloading sequences and annotation data. Five useful search interfaces consisting of BLAST search, keyword search, BLAST result-based search, GO tree-based search, and genome browser are provided. KONAGAbase is publicly available from our website (http://dbm.dna.affrc.go.jp/px/) through standard web browsers.
  
  
  CONCLUSIONS
  KONAGAbase provides DBM comprehensive transcriptomic and draft genomic sequences with useful annotation information with easy-to-use web interfaces, which helps researchers to efficiently search for target sequences such as insect resistance-related genes. KONAGAbase will be continuously updated and additional genomic/transcriptomic resources and analysis tools will be provided for further efficient analysis of the mechanism of insecticide resistance and the development of effective insecticides with a novel mode of action for DBM.
authors.affiliation: National Institute of Agrobiological Sciences, Tsukuba 305-8634, Japan. joraku@affrc.go.jp
authors.forename: Akiya
authors.initials: A
authors.lastname: Jouraku
authors.forename: Kimiko
authors.initials: K
authors.lastname: Yamamoto
authors.forename: Seigo
authors.initials: S
authors.lastname: Kuwazaki
authors.forename: Masahiro
authors.initials: M
authors.lastname: Urio
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Suetsugu
authors.forename: Junko
authors.initials: J
authors.lastname: Narukawa
authors.forename: Kazuhisa
authors.initials: K
authors.lastname: Miyamoto
authors.forename: Kanako
authors.initials: K
authors.lastname: Kurita
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanamori
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Katayose
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Noda
mesh_terms: D000818:Animals; D003196:Computer Graphics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D023281:Genomics; D020407:Internet; D008969:Molecular Sequence Data; D009036:Moths / Q000235:genetics*; D009928:Organ Specificity; D014584:User-Computer Interface