Silkworm Databases

Silkworm databases comprise of silkworm-specific information and are mainly classified as nucleotide, protein and genetic resource databases based on the core information which are further grouped into sub-categories. These databases are briefly described here.


1. Nucleotide Databases

Nucleotide databases mainly deals with nucleotide information of silkworms such as genomic sequences, expressed sequence tag (EST), transcriptomic sequences, microsatellite, microarray etc. This data can be helpful for various studies like genetic marker studies, functional and comparative genomics, phylogenetic analyses etc. Here we briefly describe the nucleotide databases available at present.

1.1. Silkworm Genome Databases

Since the generation of first genome draft of B. mori (2004), genome databases have been developed to comprise genomic data of the silkworms which are briefly described here.

Database Name

Data type

Data content

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SilkDB V 2.0

Genomic Data

428.7 Mb B.mori genomic sequences

  • 23156 scaffolds for 28 chromosomes

  • 601225 transposable elements

  • 18510 annotated gene sequences and full cDNA sequences of 212 known silkworm genes

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KAIKObase

BAC-end sequences

fosmid sequences

ESTs

  • 43,462 assembled data of B. mori
  • 81,705 BAC-end sequences
  • 174,222 fosmid-end sequences
  • 166,757 ESTs
  • 16,209 gene models
  • 1,532 SNP markers
  • 770 trait markers
  • 5,419 FPC contigs
More

 

1.2. Silkworm Gene Expression Databases

This section includes various gene expression databases which help in studying gene expression profile, alternate splicing events etc. under various conditions using approaches like next-generation sequencing (NGS), microarrays etc. These databases are briefly discussed in this section.

Database Name

Data type

Data content

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SilkBase

EST sequences

35,000 ESTs from 36 cDNA libraries More
Wild Silkbase EST sequences 57,113 ESTs More
ButterflyBase

EST sequences,

Aannotation data

273 077 ESTs of 30 different butterflies & other lepidopteran insects species. More
BmMDB Microarray data 22 987 gene probes of silkworm. More
SilkTransDB

Whole transcriptome

7-fold covarage of 3.3 gigabase (Gb) reads. More
InsectBase Integrated insect genome & trancriptome >12 millions of sequences (genomes of 138 insects, transcriptomes of 116 insects, gene sets of 61 insects, 36 gene families of 60 insects, 7,544 miRNAs of 69 insects, 96,925 piRNAs from two insects, 22,536 pathways of 78 insects, 679,881 UTR of 84 insects and 160,905 CDS of 74 insects) More

 

1.3. Microsatellite database

Microsatellites are short tandem repeats of 1-6 bp with conserved protein coding and non-coding regions which are helpful for genetic studies like fingerprinting, linkage map construction etc. Currently, two databases host silkworm microsatellite information which are described here.

Database Name

Data type

Data content

More on Database

SilkSatDB

Microsatellite data

EST sequences

Information pertaining to 12000 WGS contigs, 9300 EST and 50 genomic sequences of B. mori More
InSatDB Microsatellite data
  • Microsatellite characteristics of five fully sequenced insect genomes (Bombyx mori, Drosophila melanogaster, Anopheles gambia, Apis mellifera,Tribolium castaneum).
  • Characteristics- size (in base pairs and repeat units); genomic location (exon, intron, up-stream or transposon); nature (perfect or imperfect); and sequence composition (repeat motif and GC%)
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1.4. Silkworm Mutant Databases

Silkworm mutants are known to influence various characteristics of silkworms like biochemical, behavioural, physiological, developmental etc. These mutants play a vital role in diverse studies like enhanced production of fibroin, silk diversity, disease-related studies, gene function analyses etc. Databases comprising such information are briefly described in this section.

Database Name

Data type

Data content

More on Database

DBMP

Mutant silkworm data

Photographs of mutants (having mutantions on different chromosomes) in B. mori. More
ABURAKO EST sequences List of B. mori mutants, linkage maps. More
Bombyx Trap Database Mutant silkworm data 288 transposon insertion lines. More

 

1.5. Transposable elements database

Database Name

Data type

Data content

More on Database

BmTEdb

Transposable elements

1308 TE families

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2. Protein Databases

This section deals with protein databases which aid in understanding the silkworm proteome and occupy a crucial position in research. These databases are briefly described here.

Database Name

Data type

Data content

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Kaiko2DDB

Protein

116 2D-PAGE images of different B. mori tissues. More
SilkProt

Annotated protein

Annotated Silkworm Proteins. More
SilkPPI

Protein-protein         interaction data

7736 predicted protein-protein interaction pairs (2700 unique proteins). More
SilkTF

Transcription factor

Transcription factors of B. mori. More
Insect Proteome Database, Silkworm

Silkworm Proteome

Information can be searched through Spot ID More

 


3. Silkworm Genetic Resource databases

Apart from silkworm nucleotide and protein databases, databases comprising information on genetic resources like silkworm strains, varieties, feeding behavior, rearing strategies etc. from a part of seri-informatics DB. This section deals with such genetic resource databases like Silkworm Gene Resources Database (SGRD) and SilkwormBase.

Database Name

Data type

Data content

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SGRD

Characteristic information (Varieties, Strains)

Characterization information of 321 silkworm varieties More
SilkwormBase
  • Characteristic information
  • Genetic stock resources
  • Genetic resource stock information
  • Mutant genetic information
  • Reference information (focused on references related to the gene name)
  • Distribution request information
  • Related site links, etc.
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4. Insect Pathway Databases

It includes database discussing about the pathways of insects including Lepidopteran insects (e.g. Bombyx mori).

Database Name

Data type

Data content

More on Database

iPathDB

Pathway data

Pathways of molecular interactions of 52 insects. More