TRANSCRIPTOMICS a i Massively parallel sequencing of RNA, known as RNA- creasingly attractive for quantitative studies of differen-

provides unprecedented access to sequence and ex-pression variation in the transcriptome [1,2] and allows for additional insights into alternative splicing [3], cis vs. trans gene regulation [4], and micro-RNA dynamics [5]. RNA-Seq experiments for gene expression analysis typic-ally involve mapping 10’s of millions of short sequencing reads onto the reference dataset (scaffold) of a model species, whose genome has been sequenced and gene models determined [6]. As next generation sequencing becomes more affordable (see [7] for an insightful tial gene expression in non-model species, for which there is often much knowledge of the evolution and ecology but little or no genomic resources. The non-model species community is rapidly harnes-sing the transcriptome, with an explosion of RNA-Seq studies published over the past 5 years, predominantly using the longer sequencing reads of the 454 FLX tech-nology for the generation of EST databases containing sequence and SNP information [8-12]. This community is now also beginning to use the Illumina platform with excellent results, further decreasing the cost for tran-scriptome database construction and SNP identification * Correspondence