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Background  The moss  Physcomitrella patens  is an emerging plant model system due to its high rate of homologous recombination, haploidy, simple body plan, physiological properties as well as phylogenetic position. Available EST data was clustered and assembled, and provided the basis for a genome-wide analysis of protein encoding genes.    Results  We have clustered and assembled  Physcomitrella patens  EST and CDS data in order to represent the transcriptome of this non-seed plant. Clustering of the publicly available data and subsequent prediction resulted in a total of 19,081 non-redundant ORF. Of these putative transcripts, approximately 30% have a homolog in both rice and  Arabidopsis  transcriptome.  More than 130 transcripts are not present in seed plants but can be found in other kingdoms. These potential "retained genes" might have been lost during seed plant evolution. Functional annotation of these genes reveals unequal distribution among taxonomic groups and intriguing putative functions such as cytotoxicity and nucleic acid repair.  Whereas introns in the moss are larger on average than in the seed plant  Arabidopsis thaliana , position and amount of introns are approximately the same. Contrary to  Arabidopsis , where CDS contain on average 44% G/C, in  Physcomitrella  the average G/C content is 50%. Interestingly, moss orthologs of  Arabidopsis  genes show a significant drift of codon fraction usage, towards the seed plant. While averaged codon bias is the same in  Physcomitrella  and  Arabidopsis , the distribution pattern is different, with 15% of moss genes being unbiased.  Species-specific, sensitive and selective splice site prediction for  Physcomitrella  has been developed using a dataset of 368 donor and acceptor sites, utilizing a support vector machine. The prediction accuracy is better than those achieved with tools trained on  Arabidopsis  data.    Conclusion  Analysis of the moss transcriptome displays differences in gene structure, codon and splice site usage in comparison with the seed plant  Arabidopsis . Putative retained genes exhibit possible functions that might explain the peculiar physiological properties of mosses.  Both the transcriptome representation (including a BLAST and retrieval service) and splice site prediction have been made available on   , setting the basis for assembly and annotation of the  Physcomitrella  genome, of which draft shotgun sequences will become available in 2005.

Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens