the silkworm ( bombyx mori ) , domesticated over the last 5000 years from a wild progenitor bombyx mandarina ( 1 ) , is an important source of livelihood for subsistence farmers engaged in silk production in many countries .
it is believed to be a central model for lepidopteran genomics and genetics , and second only to fruitfly ( drosophila melanogaster ) ( 2 ) as an insect model for genetic studies ( 3 ) .
as many basic physiological processes of insects are conserved through evolution , study of silkworm will help further elucidate the function of gene homologs and facilitate studies of insect domestication , morphogenesis , endocrinology , reproduction , behavior and immunity .
bombyx mori has an estimated haploid nuclear genome size of 530 mb ( 4 ) broken into 28 chromosomes .
a 3x coverage draft sequence was reported previously ( 5 ) and many expressed sequence tag ( est ) sequences have been released ( 6 ) .
many other resources will be generated by the international lepidopteran genome project ( http://www.ab.a.u-tokyo.ac.jp/lep-genome ) . at the beijing genomics institute ( bgi ) , the major genome sequencing center in china
the silkworm genome sequence is an important contribution to functional genomics for the silkworm and comparative and functional genomics for lepidopteran species , and will provide a solid foundation for integrating biological information for lepidopteran and even insects in general . in order to facilitate the usage of most up - to - date knowledge about the silkworm genome , we developed the silkworm knowledgebase ( silkdb ) as a highly integrated information system for silkworm data storage , retrieval , visualization and analysis .
the current version of silkdb is focused on assembling contigs and anchoring contigs onto scaffolds based on mapped genetic markers and bac - based physical maps . in the process , we have developed software packages for sequence assembly , identification and annotation of genes and transposable elements ( tes ) . we utilize silkworm as a framework genome to organize information for other lepidoptera , which represent a diverse and important group of insect pests in agriculture , so as to bridge the model insect and its family members .
silkdb , together with its database , search engine and genome - oriented mapview provides both an information resource and a comparative analysis workbench for genomic research of silkworm and other insects .
owing to the complexity and the large - scale nature of the genomic data , the strategy of comprehensive organization and effective management are of essence for successive analyses . in silkdb , we organize the genomic data in three different modules of scaffold / contig , gene / cdna and te classes , and link the data of different modules through genome - oriented mapview . in scaffold module , silkdb contains the 428.7 mb b.mori genomic sequences covering 90.9% of all known silkworm genes .
the raw sequences were produced by using a whole genome shotgun ( wgs ) ( 7 ) technique and sequence reads were assembled by using an updated version of our reps software ( 8) . there are 23  156 scaffolds for the 28 chromosomes .
the average contig and scaffold sizes , by using n50 statistics , are 12.5 and 26.9 kb , respectively .
genomic sequences were annotated for gene content by using bgf ( bgi gene finder ) and database searches against public resources .
bgf is a self - developed ab initio program based on genscan ( 9 ) and fgenesh ( 10 ) , and was successfully utilized for our rice genome annotation ( 11 ) .
after correction of partial and erroneous predictions , the estimated gene count is 18  510 , which exceeds the 13  379 genes reported for d.melanogaster ( 12 ) .
interpro domains ( 13 ) were annotated by interproscan release 7.0 and functional assignments were mapped onto gene ontology ( go ) ( 14 ) .
to further the study of silkworm genome biology , we investigated the biologically important genes in comparison with spider and butterfly , such as silk gland , wing patterning , development , immunity and defense , hormones and receptors , etc .
besides the 18  510 annotated genes , the gene module hosts a collection of 212 known silkworm genes ( with full - length cdna sequences ) from genbank ( 15 ) , 16  425 est clusters based on our sequencing of 80  470 ests from different b.mori tissues , 554 genbank genes of other lepidoptera and 521 b.mori homologs of other lepidopteran genes .
snps mined from the b.mori est sequences ( 16 ) were collected and mapped onto the genome .
a set of b.mandarina ests was also produced , clustered and compared with the b.mori dataset for domestication study .
genome expansion is believed to be due to te insertions . to explore the increase in genome size from fruitfly ( 116.8 mb ) ( 17 ) to silkworm ( 428.7 mb ) , we applied repeatmasker ( http://www.repeatmasker.org/ ) for identifying tes and tagging te classes .
a total of 601  225 tes were identified , most of which are from a single gypsy - ty3-like retrotransposon ( 18 ) .
classes of tes and their detailed information are stored in the third module , the te_class module .
a simple way for users to access data stored in the silkdb database is through the  data module , where users can get an overview of the data content , data statistics and the correlations between each data type .
mapview and search engine are two self - developed tools built on top of the database for rapid visualization and querying of the data at many levels . as an efficient visualization tool
, mapview currently displays the b.mori genome assembly on the scaffold scale with sequence contigs aligned to , and allows users to browse a series of tracks aligned with the genomic sequence ( figure 1 ) .
users may center the map upon a point on the scaffold of interest and expand to obtain a more detailed view of genetic markers , predicted genes , cdnas , est clusters of both the domestic and wild silkworm , and classes of tes .
b.mori gene homologs of other lepidoptera are also marked out with distinct color - coding .
every sequence record is linked to several display options in mapview system . a text - based tabular report for each element contained in the visualization system
cross - referenced links to related database entries , such as interpro , go and genbank , are also provided if available .
the silkdb search engine is the entry point for searching the major data types stored in the silkdb .
it provides two kinds of searches for users : keyword - based subject search and blast - based homology search , including searches for scaffolds , contigs , genes , cdnas , classes of tes , etc .
users can define concrete limitations to extract records that are best suited to their research needs .
the front end consists of a set of jsp scripts running on tomcat web server .
a large set of java servlets and javabeans mediate the user 's interaction with the database . to handle the large amount of yet complex silkworm genome data , we developed a standard set of genome - based bio - xml format that lays the foundation for our research work and allows silkdb to accommodate the fast - accumulating data and to integrate new data types when encountered .
we are aiming at building a genomic information resource and comparative analysis workbench for silkworm with an intention to expand to other lepidoptera and model insects .
continued efforts will be made for the improvement of data quality , including anchoring scaffolds onto b.mori chromosomes , improving functional annotations based on phenotypically identified mutants and gene expression at the transcription and translation levels , updating est clusters as more data are generated and annotating the clusters with respect to potential encoded protein products . besides the timely updated silkworm genome information , silkdb has been constantly incorporating more data , as they become available , from other lepidoptera genomes , and different types of biological data , such as phenotype and gene expression data .
refinement of the system and addition of new applications are continuous efforts for the silkdb project .
we will introduce into silkdb a versioning system and references around different versions . in the near future
, it will be possible for users to retrieve the data of different versions , trace up and locate changes of a given entity between different versions . a key enhancement to comparative analysis
will be the development of a comparative map viewer , allowing users to evaluate the alignment of conserved regions with alternative views of genome evolution .
based on the comparative map viewer , further comparative studies on genomic sequences between lepidoptera , d.melanogaster , anopheles gambiae ( 19 ) , caenorhabditis elegans ( 20 ) , and other invertebrates will be conducted for the study of lepidopteran - specific genes , many of which are potential candidates for targets of lepidopteran - selective insecticides , and will help further our understanding of the molecular mechanism of genetic diversity among insects .
this project was funded by chinese academy of sciences ( kscx2-sw-223 ) , national development and reform commission , ministry of science and technology ( 2002aa104250 ; 2002aa234011 ; 2001aa231061 ; 2001aa231011 ; 2001aa231101 ; 2004aa231050 ; 30200163 ; 90208019 ) , china national grid ( 2002aa104250 ) and 863 high technology foundation of china ( 2004aa2z1020 ) .
 the silkworm knowledgebase ( silkdb ) is a web - based repository for the curation , integration and study of silkworm genetic and genomic data . with the recent accomplishment of a 6x draft genome sequence of the domestic silkworm ( bombyx mori ) 
 , silkdb provides an integrated representation of the large - scale , genome - wide sequence assembly , cdnas , clusters of expressed sequence tags ( ests ) , transposable elements ( tes ) , mutants , single nucleotide polymorphisms ( snps ) and functional annotations of genes with assignments to interpro domains and gene ontology ( go ) terms . 
 silkdb also hosts a set of ests from bombyx mandarina , a wild progenitor of b.mori , and a collection of genes from other lepidoptera . 
 comparative analysis results between the domestic and wild silkworm , between b.mori and other lepidoptera , and between b.mori and the two sequenced insects , fruitfly and mosquito , are displayed by using b.mori genome sequence as a reference framework . 
 designed as a basic platform , silkdb strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in - depth comparative studies . 
 silkdb is publicly accessible at http://silkworm.genomics.org.cn . 
INTRODUCTION
DATA CONTENT AND SOURCING
ACCESS AND WEB QUERY INTERFACE
SYSTEM IMPLEMENTATION
FUTURE DEVELOPMENTS
ACKNOWLEDGEMENTS