Putative retained genes exhibit possible functions that might explain the peculiar physiological properties of mosses.īoth 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.įlowering plants have developed from a common ancestor with mosses, liverworts, ferns, and gymnosperms over the last 450 million years. ConclusionĪnalysis of the moss transcriptome displays differences in gene structure, codon and splice site usage in comparison with the seed plant Arabidopsis. The prediction accuracy is better than those achieved with tools trained on Arabidopsis data.

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. While averaged codon bias is the same in Physcomitrella and Arabidopsis, the distribution pattern is different, with 15% of moss genes being unbiased. Interestingly, moss orthologs of Arabidopsis genes show a significant drift of codon fraction usage, towards the seed plant. Contrary to Arabidopsis, where CDS contain on average 44% G/C, in Physcomitrella the average G/C content is 50%. 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. Functional annotation of these genes reveals unequal distribution among taxonomic groups and intriguing putative functions such as cytotoxicity and nucleic acid repair. These potential 'retained genes' might have been lost during seed plant evolution. More than 130 transcripts are not present in seed plants but can be found in other kingdoms.

Of these putative transcripts, approximately 30% have a homolog in both rice and Arabidopsis transcriptome. Clustering of the publicly available data and subsequent prediction resulted in a total of 19,081 non-redundant ORF. We have clustered and assembled Physcomitrella patens EST and CDS data in order to represent the transcriptome of this non-seed plant. Available EST data was clustered and assembled, and provided the basis for a genome-wide analysis of protein encoding genes. 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.

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