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• Science 306, 1937-1940 (2004)( PDF )

• Nucleic Acids Research 33, 399-402 (2005)( PDF )

About the Silkworm Genome Database

       The silkworm, Bombyx mori, has been used for silk production for about 5,000 years. Currently,it is one of the most economically important, beneficial insects in many developing countries owing to its ease of large-scale propagation and textile-industry utilization. The silkworm can also be used as a bioreactor for proteinaceous drugs and vaccines, as well as a source of biomaterials. On the other hand, silkworm is also one of the best-characterized models for insect biochemical, genetic and genomic studies, because of its large size, complex metabolism and the abundance of mutants [1]. The silkworm is a pioneering animal in the history of biology, leading to the first verification of the Mendel's Law in animals (1906), the first discovery of molting hormone (1940), and the first identification of pheromone (1959). Also, it is unique in being a domesticated insect that is completely dependent on humans for survival and reproduction. Yet, it could hybridize with its nearest wild relative, making them an excellent model for studying the genetics of domestication.

       Silkworm has 28 chromosomes and is estimated a haploid nuclear genome size of 530-Mb. Recently, a large and diverse collection of genetic markers, including RAPDs, RFLPs and SSRs, have been developed and mapped. The combined map contains more than a thousand molecular markers, at an average spacing of 2-cM (or about 500-Kb). In addition, among the more than 400 visible phenotypes, nearly 200 are assigned to linkage groups. Interestingly, some genes related to cocoon color, virus resistance and wingless mutation have been positionally cloned and analyzed.

       The silkworm genome project experienced three phases. Firstly, a large number of expressed sequence tag (EST) sequences for silkworm multiple tissues have been sequenced and released in 2002. Secondly, 6x and 3x draft genome sequences were independently generated based on whole genome shotgun (WGS) sequencing by Chinese and Japanese groups in 2004, respectively [2-3]. Finally, Chinese and Japanese groups worked jointly and used the merged WGS reads, together with newly generated fosmid- and BAC-end data, to assemble a high-quality genome sequence of the silkworm in 2007.

       The new silkworm genome assembly has a size of 432Mb and has the best continuity (~ 15.5Kb and 3.7Mb in N50 contig and scaffold size, respectively). Using a high-density SNP linkage map consisting of 1,577 markers, about 87.4% of the scaffold sequences were anchored to all 28 chromosomes [4]. Among the 767 cDNAs collected from GenBank, 96% (738) could be fully aligned on the genome with correct order and exon orientation. The estimated gene count is 14,623, which is slightly higher than Drosophila melanogaster (14,039 genes) and 44% higher than Apis mellifera (10,157 genes). Moreover, approximately 47% of silkworm genes have EST expression evidence, 38% have GO classifications, and 76% have identifiable Drosophila melanogaster homologues.

       To manage the silkworm genome sequence data, the SilkDB was constructed by Chinese group in 2004 after the completion of 6x draft sequence [5]. Along with the performation of silkworm functional genomics research, huge functional data of the silkworm genes have produced. To better deposit the newly assembled silkworm genome sequence and related functional data and to facilitate users to access the relative information, we redeveloped the SilkDB. It is our hope that the SilkDB will provide more useful help for silkworm and insect researchers.

References
      [1]Goldsmith MR, Shimada T, Abe H: The genetics and genomics of the silkworm, Bombyx mori. Annu Rev Entomol 2005, 50:71-100.
      [2]Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, et al.: A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 2004, 306:1937-1940.
      [3]Mita K, Kasahara M, Sasaki S, Nagayasu Y, Yamada T, Kanamori H, Namiki N, Kitagawa M, Yamashita H, Yasukochi Y, et al.: The genome sequence of silkworm, Bombyx mori. DNA Res 2004, 11:27-35.
      [4]Yamamoto K, Nohata J, Kadono-Okuda K, Narukawa J, Sasanuma M, Sasanuma SI, Minami H, Shimomura M, Suetsugu Y, Banno Y, et al.: A BAC-based integrated linkage map of the silkworm Bombyx mori. Genome Biol. 2008, 9:R21.       [5]Wang J, Xia Q, He X, Dai M, Ruan J, Chen J, Yu G, Yuan H, Hu Y, Li R, et al.: SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res 2005, 33:D399-402.