WildSilkbase: An EST database of wild silkmoths
<p>Abstract</p> <p>Background</p> <p>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 interaction...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-07-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/338 |
| _version_ | 1819141202037964800 |
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| author | Nagaraju J Shimada Toru Daimon Takaaki Tomar Archana Arunkumar KP |
| author_facet | Nagaraju J Shimada Toru Daimon Takaaki Tomar Archana Arunkumar KP |
| author_sort | Nagaraju J |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Description</p> <p>WildSilkbase is a catalogue of ESTs generated from several tissues at different developmental stages of 3 economically important saturniid silkmoths, an Indian golden silkmoth, <it>Antheraea assama</it>, an Indian tropical tasar silkmoth, <it>A. mylitta </it>and eri silkmoth, <it>Samia cynthia ricini</it>. 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 <url>http://www.cdfd.org.in/wildsilkbase/</url>.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-22T11:50:42Z |
| format | Article |
| id | doaj.art-9e5ea1f9a85142e2856c0dcf2984d290 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-22T11:50:42Z |
| publishDate | 2008-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-9e5ea1f9a85142e2856c0dcf2984d2902022-12-21T18:27:00ZengBMCBMC Genomics1471-21642008-07-019133810.1186/1471-2164-9-338WildSilkbase: An EST database of wild silkmothsNagaraju JShimada ToruDaimon TakaakiTomar ArchanaArunkumar KP<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Description</p> <p>WildSilkbase is a catalogue of ESTs generated from several tissues at different developmental stages of 3 economically important saturniid silkmoths, an Indian golden silkmoth, <it>Antheraea assama</it>, an Indian tropical tasar silkmoth, <it>A. mylitta </it>and eri silkmoth, <it>Samia cynthia ricini</it>. 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 <url>http://www.cdfd.org.in/wildsilkbase/</url>.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/9/338 |
| spellingShingle | Nagaraju J Shimada Toru Daimon Takaaki Tomar Archana Arunkumar KP WildSilkbase: An EST database of wild silkmoths BMC Genomics |
| title | WildSilkbase: An EST database of wild silkmoths |
| title_full | WildSilkbase: An EST database of wild silkmoths |
| title_fullStr | WildSilkbase: An EST database of wild silkmoths |
| title_full_unstemmed | WildSilkbase: An EST database of wild silkmoths |
| title_short | WildSilkbase: An EST database of wild silkmoths |
| title_sort | wildsilkbase an est database of wild silkmoths |
| url | http://www.biomedcentral.com/1471-2164/9/338 |
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