Abstract
As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Highlights
Molluscs are important members of many terrestrial and aquatic ecosystems, where they can be dominant herbivores or important predators
The mollusc shell is a product of active biomineralization, the enzymology of which is of interest to synthetic biology, aquaculture and climate science
Improved understanding of all of these issues and questions can be gained through the application of genomic and post-genomic methodologies to target species of molluscs, and through comparison of mollusc genes and genomes
Summary
Molluscs are important members of many terrestrial and aquatic ecosystems, where they can be dominant herbivores or important predators. Data are hosted in taxon-specific databases, such as FlyBase [6] or WormBase [7] These offer a feature-rich presentation and analysis ecosystem that can focus on meeting the specific needs of their research communities. Owing to their multiple advantages, taxon-specific databases have been developed for nonmodel organisms, such as VectorBase [8], Avianbase [9] and Lepbase [10]. This tiered system of databases, from Tier 1 (local, often private, single-species or single-analysis resources) through Tier 2 (multi-species databases) and Tier 3 (panspecies databases such as Ensembl) [11] delivers to the needs of the science community. We discuss the features of MolluscDB and highlight its utility by using it to support analyses of mollusc phylogeny, of gene family evolution and of genes associated with biomineralization
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