Arunkumar K P, Tomar Archana, Daimon Takaaki, Shimada Toru, Nagaraju J
Centre of Excellence for Genetics and Genomics of Silkmoths, Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, ECIL road, Nacharam, Hyderabad-500 076, India.
BMC Genomics. 2008 Jul 17;9:338. doi: 10.1186/1471-2164-9-338.
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.
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/.
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.
功能基因组学在蚕生物学中具有独特的前景，可用于鉴定参与多种生物学功能的基因，这些功能包括：丝的合成与分泌、性别决定途径、昆虫与病原体的相互作用、卵壳发生、分子钟。野生蚕蛾几乎未曾成为详细科学研究的对象，这主要是因为缺乏这些物种的分子和遗传数据。作为第一步，在本研究中，我们在三种具有经济重要性的野生蚕蛾物种中生成了大规模表达序列标签（EST）。为了使这些资源可供全球科学界使用，开发了一个名为“WildSilkbase”的EST数据库。
WildSilkbase是一个来自三种具有经济重要性的天蚕蛾不同发育阶段多个组织的EST目录，这三种天蚕蛾分别是印度金蚕蛾（柞蚕）、印度热带柞蚕蛾（蓖麻蚕）和蓖麻蚕。目前该数据库有57,113个EST，它们被聚类并组装成4,019个重叠群和10,019个单拷贝序列。数据可以使用标准网页浏览器进行浏览和下载。用户可以通过BLAST查询、关键词或基因本体查询来搜索数据库。在BLAST页面有选项可对物种、组织和发育阶段特异性EST进行搜索。WildSilkbase的其他功能包括cSNP发现、GO查看器、同源物查找器、SSR查找器以及与所有其他相关数据库的链接。WildSilkbase可从http://www.cdfd.org.in/wildsilkbase/免费获取。
在三种野生蚕蛾物种中总共鉴定出14,038个假定的单基因。这些基因为深入了解野生蚕蛾的功能和进化研究提供了重要资源。我们相信WildSilkbase对于所有从事比较基因组学、功能基因组学和分子进化领域研究的人员，特别是从事昆虫物种基因发现、基因组织、转座元件和基因组变异性研究的人员将极其有用。
