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. 2021 May 24;376(1825):20200157.
doi: 10.1098/rstb.2020.0157. Epub 2021 Apr 5.

MolluscDB: a genome and transcriptome database for molluscs

Carlos Caurcel  1 , Dominik R Laetsch  1 , Richard Challis  1   2 , Sujai Kumar  1   2 , Karim Gharbi  1   3 , Mark Blaxter  1   2
Affiliations

MolluscDB: a genome and transcriptome database for molluscs

Carlos Caurcel et al. Philos Trans R Soc Lond B Biol Sci. .

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'.

Keywords: database; genome; molluscs; protein families; shell matrix proteins; transcriptome.

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Figures

Figure 1.
Figure 1.
Protein families in species represented in MolluscDB. (a) Stacked histogram of proteins in each taxon analysed assigned to: ‘shared’: proteins in clusters containing proteins from multiple taxa; ‘specific’: proteins in clusters containing two or more proteins from a single proteome; and ‘singleton’: proteins in single protein clusters. (b) Frequency plot of cluster size in the OrthoFinder clustering of 214 608 orthogroups. (Online version in colour.)
Figure 2.
Figure 2.
Phylogenetic tree of taxa in MolluscDB. Multilocus phylogeny of the species analysed. Support is 100 at all nodes except indicated.
See this image and copyright information in PMC

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