Comparative Transcriptomics of North American Cyprinids: 454 Transcriptome Sequencing of a Non-Model Minnow and Comparison with Model Minnow Species

Efforts toward advancing our understanding of adaptation of fishes to their environment are hampered by a lack of genomic resources for non-model species.  For the post-genomics revolution to reach full fruition, we need to extend resources developed for model organisms (e.g., zebrafish, Danio rerio) for use in non-model species.  The recent advent of next-generation DNA sequencing has paved the way for genome-scale studies of local adaptation, gene expression, organismal performance, etc., in aquatic ecosystems.  In this study, we used 454 FLX sequencing to characterize the transcriptome of Rio Grande silvery minnow (Hybognathus amarus), a federally endangered species for which no genomic resources were available.  Next-generation sequencing of brain, liver and gonad cDNA yielded over 350,000 sequence reads which assembled into 50,680 contigs with mean length of 359 base pairs.  Contigs were subjected to Blast searches and gene-ontology mapping, and were searched for high-confidence single nucleotide polymorphisms (SNPs).  Additionally, contigs were mapped to the zebrafish genome sequence and other cyprinid cDNA libraries (fathead minnow, common carp, etc.) to determine regions of conservation and divergence among species.  This study represents a critical first step toward developing a comparative genomics database for North American cyprinid fishes that will be an invaluable resource for future genetic studies.