News

  • Fixed a bug (2013-07-26)
    • FPKM values of part of unigene sequences (PXUG_V1_030696 - PXUG_V1_084570) were incorrectly set to 0 in search result table and in sequence information pages.
      This bug is now fixed.
  • KONAGAbase paper was published in BMC Genomics (2013-07-08)
  • Various updates (2013-03-29)
    • Updated predicted genes by using additional gene prediction software programs
    • Updated putative gene set with the updated predicted genes
    • GBrowse is now available. Putative gene set, predicted genes, and unigene can be viewed in the genome browser
    • Added a putative unknown gene set which has no homologous genes/domains (novel genes might be included in the gene set)
    • Link to old KONAGAbase [click here]
  • KONAGAbase is publicly available (2012-11-13)

Introduction

KONAGAbase is a genomic database of the diamondback moth (Plutella xylostella) (KONAGA is the Japanese word for the diamondback moth).
The database currently provides the following sequence data with userful annotation information by BLAST, HMMER3, and Blast2GO:
(For detailed information of each sequence, please click Download tab)
  • Genome Sequence (strain: PXS (Bacillus thuringiensis toxin susceptible))
    1. Assembled WGS sequences (N50: 2,273) generated from 454 WGS reads (coverage 5x)
    2. Predicted gene's coding sequences (34,890 sequences) identified from the assembled WGS sequences
    3. Putative repeat sequences (6,310 sequences) identified from the assembled WGS sequences
  • Transcriptome Sequence
    1. EST/mRNA sequences (37,340 sequences)
      1. 35,618 EST sequences: midgut, egg, and testis of 4th instar larvae (strain: PXS) by ABI 3730
      2. 1,722 EST/mRNA sequences retrieved from NCBI database
    2. RNA-seq contigs (147,370 sequences) generated from HiSeq 2000 single reads (20Gbp mRNA-seq: whole body of 4th instar larvae, strain: PXS)
    3. Unigene sequences (84,570 sequences) which are generated by clustering and assembling the EST/mRNA sequences and the RNA-seq contigs
  • Putative gene set (32,800 sequences): a set of representative sequences derived from the predicted gene CDSs and unigenes.
To access the sequence data, Rich-GUI based web interfaces are provided for browsing, searching and downloading the data in the database.
  • To do BLAST search against the sequences of this database, click BLAST tab.
  • To search sequence by keyword, BLAST result, GO (Gene Ontology) terms tree, etc., click Search tab.
    (In the keyword search, list of all sequences are available by invoking a search without a keyword.)
  • To search genome sequences by a genome browser, click GBrowse tab.
  • To download FASTA files of the sequences, click Download tab.
  • Help message will be displayed by clicking "?" icon in each search form.

BLAST Search Form

BLAST search against various sequences of Plutella xylostella

Click "?" icon for help message
Select sequence dataset
Query sequence

Enter one nucleotide FASTA sequence (the first line starts with '>' can be omitted)

BLAST program
Max target sequences
Expectation value
Filters
Click here to toggle Advanced Options

GBrowse

Download FASTA file

Download Unigenes (RNA-seq contigs and EST/mRNA sequences were clustered and assembled)

  • Unigenes [zipped fasta] (nucleotide) (84,570 sequences), [zipped fasta] (predicted protein) (84,562 sequences)
    click here to toggle detailed information

Download RNA-seq contigs

  • RNA-seq contigs [zipped FASTA] (147,370 sequences)
    click here to toggle detailed information

Download ESTs/mRNAs

  • ESTs/mRNAs [zipped FASTA] (37,340 sequences)
    click here to toggle detailed information

Download WGS read sequences

  • WGS read sequences (QV>20) [zipped FASTA] (Roche 454 FLX Titanium/5,082,983 sequences/1,925,467,458 bp/avg 378.8bp)

Download Assembled WGS sequences

  • Assembled WGS sequences[zipped fasta] (365Mbp: 88,530 contigs + 246,244 degenerate contigs + 106,455 singletons)
    click here to toggle detailed information

Download predicted gene CDSs

  • Predicted gene CDSs (version 2) [zipped fasta](nucleotide), [zipped fasta] (protein) (34,890 sequences)
    click here to toggle detailed information
  • OLD version
    • Predicted gene CDSs (version 1) [zipped fasta](nucleotide), [zipped fasta](protein)
      click here to toggle detailed information

Download putative gene set (Unigene sequences and predicted gene CDSs were merged)

  • Putative gene set (version 2) [zipped fasta](nucleotide), [zipped fasta] (predicted protein) (32,800 sequences)
    click here to toggle detailed information
  • Putative unknown gene set [zipped fasta] (nucleotide) (39,781 sequences), [zipped fasta] (predicted protein) (39,774 sequences)
    click here to toggle detailed information
  • OLD version
    • Putative gene set (version 1) [zipped fasta]
      click here to toggle detailed information

Download Putative Repeat Sequences

  • Putative repeat sequences [zipped FASTA] generated from the assembled WGS sequences by RepeatScout (6,310 sequences/avg. 304.0bp)
    • Putative repeat sequences were de novo identified from the assembled WGS sequences by using RepeatScout.

About Us

KONAGAbase is developed and hosted by Insect Genome Research Unit of Agrogenomics Research Center at National Institute of Agrobiological Sciences.

The development of KONAGAbase is supported by grant-in-Aid for Scientific Research (B) (22380041).

Please cite this database as:

Jouraku A, Yamamoto K, Kuwazaki S, Urio M, Suetsugu Y, Narukawa J, Miyamoto K, Kurita K, Kanamori H, Katayose Y, Matsumoto T, Noda H:
KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella. BMC Genomics 2013 14:464.

Contact

If you have any problems or questions, please contact us by email.

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