Transcriptome analysis using high-throughput short-read sequencing technology is straightforward when the sequenced genome is the same species or extremely similar to the reference genome. We present an analysis approach for when the sequenced organism does not have an already sequenced genome that can be used for a reference, as will be the case of many non-model organisms. As proof of concept, data from Solexa sequencing of the polyploid plant Pachycladon enysii was analysed using our approach with its nearest model reference genome being the diploid plant Arabidopsis thaliana. By using a combination of mapping and de novo assembly tools we could determine duplicate genes belonging to one or other of the genome copies. Our approach demonstrates that transcriptome analysis using high-throughput short-read sequencing need not be restricted to the genomes of model organisms.
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