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 http://www.cosmoss.org, setting the basis 
for assembly and annotation of the Physcomitrella genome, of which draft shotgun 
sequences will become available in 2005.