Transcriptome-based genetic marker development for non-model organisms

Authors: Nicholas G. Davis, Justin T. Page, Dennis K. Shiozawa

Year: 2012 (xliv)

Abstract

Population genetic and phylogenetic research on non-model organisms has often been limited by having too few genes available. Next generation sequencing techniques are eliminating that barrier. Using transcriptomes in combination with Illumina sequencing technology, Trinity assembly software, custom PERL pipeline scripts, and Primer3 primer prediction software, we produced and analyzed 6 Ephemeropteran (Mayfly) and 7 Plecopteran (Stonefly) transcriptomes in an attempt to identify conserved homologous genetic markers. We found 61 homologous genes for the insect order Ephemeroptera and 79 homologous genes for the insect order Plecoptera. Primer sets designed using the homologous gene alignments will be validated using PCR on representatives for all families within their respective orders and the sequence data will be used to construct new phylogenies and evaluate previous ones. These primers represent an enormous increase in the marker set for these two orders of insects. These techniques are easily translatable for work on fishes and other aquatic fauna and will soon be applied in our lab to Western North American fishes, leeches, snails, and amphipods.