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. 2008 Jul 17;9:338.
doi: 10.1186/1471-2164-9-338.

WildSilkbase: An EST Database of Wild Silkmoths

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Free PMC article

WildSilkbase: An EST Database of Wild Silkmoths

K P Arunkumar et al. BMC Genomics. .
Free PMC article

Abstract

Background: Functional genomics has particular promise in silkworm biology for identifying genes involved in a variety of biological functions that include: synthesis and secretion of silk, sex determination pathways, insect-pathogen interactions, chorionogenesis, molecular clocks. Wild silkmoths have hardly been the subject of detailed scientific investigations, owing largely to non-availability of molecular and genetic data on these species. As a first step, in the present study we generated large scale expressed sequence tags (EST) in three economically important species of wild silkmoths. In order to make these resources available for the use of global scientific community, an EST database called 'WildSilkbase' was developed.

Description: WildSilkbase is a catalogue of ESTs generated from several tissues at different developmental stages of 3 economically important saturniid silkmoths, an Indian golden silkmoth, Antheraea assama, an Indian tropical tasar silkmoth, A. mylitta and eri silkmoth, Samia cynthia ricini. Currently the database is provided with 57,113 ESTs which are clustered and assembled into 4,019 contigs and 10,019 singletons. Data can be browsed and downloaded using a standard web browser. Users can search the database either by BLAST query, keywords or Gene Ontology query. There are options to carry out searches for species, tissue and developmental stage specific ESTs in BLAST page. Other features of the WildSilkbase include cSNP discovery, GO viewer, homologue finder, SSR finder and links to all other related databases. The WildSilkbase is freely available from http://www.cdfd.org.in/wildsilkbase/.

Conclusion: A total of 14,038 putative unigenes was identified in 3 species of wild silkmoths. These genes provide important resources to gain insight into the functional and evolutionary study of wild silkmoths. We believe that WildSilkbase will be extremely useful for all those researchers working in the areas of comparative genomics, functional genomics and molecular evolution in general, and gene discovery, gene organization, transposable elements and genome variability of insect species in particular.

Figures

Figure 1
Figure 1
WildSilkbase organisation and implementation.
Figure 2
Figure 2
Web-shots of the database showing WildSilkbase query options, keyword search, homologue finder, SSR finder, GO viewer, BLAST search, cSNP data and download option.
Figure 3
Figure 3
Gene Ontology representation of A. assama and A. mylitta clusters is shown for each organizing principle of GO: biological process, cellular component and molecular function. The chart is based on percentage representation of GO mappings.
Figure 4
Figure 4
Percentage representation of gene ontology (GO) mappings for S. c. ricini clusters by biological process, cellular component, and molecular function.
Figure 5
Figure 5
Venn diagram illustrating the number of unigenes shared among the 3 wild silkmoths, A. assama, S. c. ricini and A. mylitta.
Figure 6
Figure 6
Venn diagrams showing the number of shared and species-specific genes among each of the 3 wild silkmoth species and 4 model insect species.

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