Approximately 8.8% of the expression in the silk glands is from the remaining SSTs. To identify the functionality of the SSTs, we used homology to both the full proteins in UniProt and to domains in PFAM. they have evolved potent arsenals of silk and venom. Spider silks are high performance materials made almost entirely of proteins, and thus represent an ideal system for investigating genome level evolution of novel Berberrubine chloride protein functions. However, genomic level resources remain limited for spiders. Results We assembled a transcriptome for the Western black widow (assembly, Spidroin, Gene family, Molecular evolution, construction of transcriptomes (e.g. [4, 5]). The transcriptomes can enable identification of functional genes without sequencing and assembling the often repetitive non-coding genomic regions (e.g., [6C10]). Additionally, sequencing mRNAs from specific tissues, developmental time points, or experimental conditions allows for rapid profiling of transcript abundance at a global scale  and analyzing phylogenetically Berberrubine chloride restricted adaptations (e.g., social phenotypes in ants  and the capsaicinoid pathway in peppers ). Spiders (Araneae) are a genome resource poor arthropod order, despite their taxonomic and ecological prominence. Araneae is one of the most species rich metazoan orders, consisting of over 44,000 described species that are found in every terrestrial ecosystem on the globe . Spiders synthesize the most diverse repertoire p21-Rac1 of functionally differentiated silk fiber types among all Berberrubine chloride the silk producing organisms. They are also by far the largest clade of venomous animals. The most closely related species with fully sequenced and annotated genomes diverged from spiders nearly 500 mya [13C16]. Unlike these fully sequenced arachnids, spiders are characterized by silk and venom production, the mechanics of which are poorly understood, due in part to the paucity of spider genomic resources. Recent studies have begun to use next generation sequencing in spiders to assemble partial transcriptomes for a tarantula, an orb-web weaver , two cobweb weavers [18, 19], and three social species in the genus synthesis of silk [24, 25], but these efforts have been hindered by a lack of understanding of the full molecular processes that create the silk fibers [26, 27]. Past molecular studies of silk have overwhelmingly focused on fiber-forming structural proteins (fibroins). The spider specific fibroins, also called spidroins, are encoded by members of a single gene family [28, 29]. Spidroin genes are known to be very large and internally repetitive (e.g., [30C33]) making them difficult to sequence and assemble assembly of deeply sequenced cDNA fragments to characterize the transcriptome of the Western black widow, (Theridiidae). The Western black widow is an attractive spider with which to investigate the genomics of silk production given their strong dragline silk  and the existing molecular characterization of this species’ spidroin encoding genes. has an estimated genome size of 1 1.3 billion bp , which while on the lower range of spider genomes, would be challenging to fully sequence. Thus far, spidroin paralogs have been described from five of the six functionally differentiated gland types in the black widow [33C35, 43, 44], including three of the six completely sequenced spidroin genes (builds a three dimensional cobweb that lacks the capture spiral. This collection of spidroin sequences can serve as a benchmark for the quality of the transcriptome and the capacity of the assembly to successfully integrate the large repetitive regions, where transcriptome assembly has traditionally struggled [45, 46]. Our goal was to construct a high quality reference database that could be used to identify tissue specific expression patterns in black widows, and to contribute to ongoing evolutionary genomics of spiders. Here, we identify and analyze genes specifically expressed in silk glands, and thus represent Berberrubine chloride candidates for silk components or involvement with silk synthesis, assembly or regulation. We evaluate the functions of these silk specific genes to generate a transcriptional program for silk glands. We also identify putative gene families to which these silk specific transcripts belong, allowing us to test if silk-restricted expression tends to evolve once, followed by gene expansions, or if, in contrast, silk-restricted expression.