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 Genome Sequencing Status

 Apr-2008 : Statistics of assembled silkworm genome
  1. Scaffold version 2.3 ( Build: 2, Version: 3)
  2. Number of chromosomes 28
  3. Sequence coverage 8.5x (WGS, BAC-end, fosmid-end)
  4. Clone coverage (BACs) 24.7x
  5. Clone coverage (fosmids) 12.6x
  6. Size of assembled scaffolds and contigs

  7. Scaffold(wo/g) Contig
    Size (bp) Number Size (bp) Number
    N50 3,716,872 37 15,506 8,077

  8. Anchoring of scaffolds onto chromosomes

  9. Anchored 87,4%
    Unanchord 12.6%

  10. Genes

  11. The estimated gene is 14,623.

  12. Repeat content

  13. The repeat library includes 1,668 ReAS de novo repetitive sequences and 17 known TEs.

    Class Number of consensus Total length (Mb) Percent of genome
    Classified 827 151.6 35.1
    Unclassifed 858 36.5 8.5
    Total 1685 188.1 43.6
 Mar-2006 : Agreement for a joint research on silkworm genome information between Japan and China
  1. Summary
  2.  The National Institute of Agrobiological Sciences (NIAS) in Japan and the Southwest University in Chongqing City, China have concluded a joint research agreement on March 24, 2006 in order to integrate the silkworm genome sequences previously generated and analyzed independently by each group and to facilitate the construction and analysis of an accurate silkworm genome information.

    Based on this agreement, it is expected that the complete silkworm genome information (about 5 billion nucleotide base pairs) will be elucidated and will make significant contribution to the development of safe agricultural chemicals against specific harmful insects and the promotion of industries related to insects.

  3. Outline of the joint research agreement
  4. 1) Both parties will perform all possible efforts to facilitate the integration of the silkworm genome sequence information.
    2) Both parties will perform the following activities:
    • Exchange of information derived from integration and analysis of silkworm genome sequence;
    • Joint announcement and publication of results derived from integration and analysis of silkworm genome sequence;
    • Prediction of genes from the silkworm genome sequence.

  5. Background
  6.  The NIAS has accumulated and currently maintains a large collection of silkworm genetic resources with detailed genetic information. For this reason, the NIAS has embarked on a large-scale analysis of the silkworm genome and has sequenced almost 80% equivalent of the entire genome. In China, a joint collaboration between the Southwestern University and Beijing Genomics Institute has decoded the silkworm genome sequence information. However, although the entire silkworm genome was independently decoded in Japan and China, some genomic regions have insufficient sequence data so that complete silkworm genome sequence information could not be obtained. Therefore by integration of the sequence data from both countries, it is expected that a highly accurate genome sequence data will become available to the scientific community.

  7. Future prospects
  8.  The integrated silkworm genome information and results of subsequent analysis will be jointly released in public databases. An international consortium will be coordinated with related researchers to facilitate structural and functional analysis of the silkworm genome. The NIAS in collaboration with Southwestern University will take the initiative towards a comprehensive analysis of the silkworm genome and gene analysis of other insects.

 Apr-2004 : An estimated 2.8 million sequence fragments equivalent to about 3 times the size of the silkworm genome were assembled by RAMEN, a new software for large scale whole genome shotgun sequencing developed by the Dept. of Computational Biology, Univ. of Tokyo. As a result, a total of about 213,000 contigs equivalent to 80% of the silkworm genome were generated. These sequence contigs were evaluated by alignment of about 11,000 Bombyx non-redundant ESTs. Almost 90% of the ESTs were identified in the whole genome sequence data. This work was a joint collaboration of the Department of Computational Biology, University of Tokyo and the National Institute of Genetics.

 Evaluation of whole-genome shotgun (WGS) sequence contigs by alignment of abut 11,000 Bombyx non-redundant ESTs. Criteria for alignment: >95% identity and >50 bp in length. Coverage was calculated as the ratio of the total length of alignments in WGS sequence contigs to the length of ESTs.

 For further details, please refer to:
Mita et al. 2004. The Genome Sequence of Silkworm, Bombyx mori.DNA Research11(1), 27-35.

 Mar-2003 : The SGP has completed a three-fold shotgun sequence of the silkworm genome estimated to be approximately 530 Mbp using a whole genome shotgun sequencing (WGS) strategy. The sequencing was performed in collaboration with the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF) and TAKARA BIO Inc. The quality of sequence data is currently being checked.