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.

在过去的三十年中，大西洋银杏（Menidia menidia）一直是生态学，进化生物学和生理学方面广泛研究的重点，但是迄今为止，缺乏基因组资源已经阻碍了对表型变异显着模式背后的分子基础的研究。在这个物种中描述过。我们在这里介绍了M. Menidia的第一个参考转录组。我们试图通过首先结合使用Trinity和CLC Genomics Workbench从头开始从尽可能多的基因中捕获单个代表性序列根据来自多个个体，组织类型和生命阶段的RNA-seq数据组装重叠群。为了减少冗余，我们基于与相关物种的序列相似性和转录本质量的计算预测，通过严格的过滤管道将合并的原始程序集传递给了严格的过滤管道，将最初> 480,000个contig的初始集合浓缩为最终的20,998个代表性contig，总计为总长度为53.3 Mb。在此最终装配中，有91％的重叠群在功能上带有推定的基因功能和基因本体（GO）术语和/或InterProScan标识符。该程序集包含完整的或几乎完整的248个高度保守的核心基因中95％以上的完整副本，这些副本在高等真核生物中呈低拷贝数，另外还有3.8％的部分拷贝，M. menidia转录组。这里提供的程序集将是将来研究的重要资源。