WildSilkbase: An EST database of wild silkmoths

KP Arunkumar 1 Archana Tomar 1 Takaaki Daimon 0 Toru Shimada 0 J Nagaraju 1 0 Department of Agricultural and Environmental Biology, The University of Tokyo , Yayoi 1-1-1, Bunkyo-ku, Tokyo 113 , Japan 1 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 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 nonavailability 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. - Background Sudden spurt in sequencing projects in recent years has resulted in exponential increase in the genome sequence repertoire of species that are close relatives of many model organisms. Availability of the sequence resources has accelerated comparative genomic analysis and has thus added to our understanding of organismal biology of these species. In fact new insights into human genome have come only after the sequences of related species such as chimpanzee, monkey and ape were published. However, in the insect order Lepidoptera, which consists of many economically important insects such as silkmoths, agriculture pests and beautiful butterflies, only the domesticated silkworm, Bombyx mori has achieved the distinction of the most well studied insect next only to Drosophila. Therefore, comparative genomics in this order is still in its infancy. Functional genomics has particular promise in silkworm biology for identifying genes involved in synthesis and secretion of silk, pathways involved in processes such as insect-pathogen interactions and sex determination mechanisms. Among lepidopterans, several databases such as Silkbase [1] for ESTs, Kaikobase [2] for whole genome sequence, Silkdb [3] for ESTs and whole genome sequence, and Silksatdb [4] for microsatellites, have been developed for B. mori. Apart from B. mori, more than 13,000 ESTs have been made available for butterflies through Butterflybase [5] and 32,217 ESTs for the pest species, Spodoptera frugiperda through Spodobase [6]. However, wild silkmoths are least represented owing largely to non-availability of genomic resources in these species. Hence, generation and utilization of genomic information from wild lepidopterans will be extremely useful in understanding these species at molecular level. The members of family Saturniidae, collectively known as saturniids, are among the largest and most spectacular of the Lepidoptera, with an estimated 1,300 to 1,500 different described species distributed worldwide [7]. The Saturniidae family includes the giant silkmoths, royal moths and emperor moths. The muga silkmoth, Antheraea assama (n = 15), confined to the North-eastern states of India, is the least understood and unique species among saturniid moths. The silk proteins of this species have not been studied so far despite their unique properties of providing golden lustre to the silk thread. Samia cynthia ricini (n = 13) a multivoltine silkworm commonly called as 'eri silkworm' is known for its white or brick-red eri silk. It is distributed in India, China and Japan. Its ecoraces (~16) are distributed across the Palaearctic and Indo-Australian biogeographic regions. The tropical Indian tasar silkmoth, Antheraea mylitta (n = 31) is a natural fauna of tropical India, represented by more than 20 well-described, genetically distinct ecoraces. Pursuing genetics and genomics of saturniids will be of significance for the following reasons: a) Typical of lepidopterans, B. mori females are heteroga metic, with a ZW chromosome constitution; males are ZZ. Sex chromosomes are considered to be under evolutionary constraints different from those of autosomes. W chromosome is reported to be strongly female determining [8]. The sex chromosome system of saturniid silkmoth A. assama, on the other hand, is ZZ/ZO as compared to ZZ/ ZW observed in other silkmoths. Comparative study of the sex determining genes, would thus reveal diverse sex determination mechanisms in silkmoths, b) Photoperiod plays an important role in the life history traits of wild silkmoths and hence it is important to investigate the genes involved in circadian rhythm, c) Silk fibres of different wild silkmoths show vast differences in their tenacity, texture, lustre and many other biophysical properties. In the light of these, it is interesting to study the genes encoding the silk proteins of wild silkmoths and compare them with those of mulberry silkmoth, and d) Information on immune response genes in these species can throw light on diversity of immune repertoir in these moths and may lead to identification of novel immune genes. The rapid and ever increasing deposition of ESTs of various organisms in dbEST database of NCBI shows the role of EST projects in advancing genomic science in eukaryotes. Considering the potential scientific benefits, in the current study we generated 57,113 ESTs in three wild silkmoth species, A. assama, S. (...truncated)