A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia

The Atlantic silverside (Menidia menidia) has been the focus of extensive research efforts in ecology, evolutionary biology, and physiology over the past three decades, but lack of genomic resources has so far hindered examination of the molecular basis underlying the remarkable patterns of phenotypic variation described in this species. We here present the first reference transcriptome for M. menidia. We sought to capture a single representative sequence from as many genes as possible by first using a combination of Trinity and the CLC Genomics Workbench to de novo assemble contigs based on RNA-seq data from multiple individuals, tissue types, and life stages. To reduce redundancy, we passed the combined raw assemblies through a stringent filtering pipeline based both on sequence similarity to related species and computational predictions of transcript quality, condensing an initial set of > 480,000 contigs to a final set of 20,998 representative contigs, amounting to a total length of 53.3 Mb. In this final assembly, 91% of the contigs were functionally annotated with putative gene function and gene ontology (GO) terms and/or InterProScan identifiers. The assembly contains complete or nearly complete copies of > 95% of 248 highly conserved core genes present in low copy number across higher eukaryotes, and partial copies of another 3.8%, suggesting that our assembly provides relatively comprehensive coverage of the M. menidia transcriptome. The assembly provided here will be an important resource for future research.