A gene family-based method for interspecies comparisons of sequencing-based transcriptomes and its use in environmental adaptation analysis

We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to implement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus mawsoni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data (available at: http://www.fishgenome.org/polarbank/) from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the comparison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diff program and operation manual can be downloaded from: http://www.fishgenome.org/download/Prodiff.rar.