Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution

Abstract

The mosses and flowering plants diverged >400 million years ago. The mosses have haploid-dominant life cycles, whereas the flowering plants are diploid-dominant. The common ancestors of land plants have been inferred to be haploid-dominant, suggesting that genes used in the diploid body of flowering plants were recruited from the genes used in the haploid body of the ancestors during the evolution of land plants. To assess this evolutionary hypothesis, we constructed an EST library of the moss Physcomitrella patens, and compared the moss transcriptome to the genome of Arabidopsis thaliana. We constructed full-length enriched cDNA libraries from auxin-treated, cytokinin-treated, and untreated gametophytes of P. patens, and sequenced both ends of >40,000 clones. These data, together with the mRNA sequences in the public databases, were assembled into 15,883 putative transcripts. Sequence comparisons of A. thaliana and P. patens showed that at least 66% of the A. thaliana genes had homologues in P. patens. Comparison of the P. patens putative transcripts with all known proteins, revealed 9,907 putative transcripts with high levels of similarity to vascular plant genes, and 850 putative transcripts with high levels of similarity to other organisms. The haploid transcriptome of P. patens appears to be quite similar to the A. thaliana genome, supporting the evolutionary hypothesis. Our study also revealed that a number of genes are moss specific and were lost in the flowering plant lineage.

Fig. 1.

Classification of A. thaliana genes according to the presence of homologous genes in other organisms. The amino acid sequences of all of the predicted genes of A. thaliana were used as the query in a tblastn similarity search with the moss, yeast, fruit fly, and cyanobacterial data sets. The outermost circle represents all of the A. thaliana genes. The inner circles, which are labeled Moss, Eukaryotes, and Cyanobacterium, represent genes that have similarity to moss contigs, budding yeast and fruit fly coding sequences, and cyanobacterium coding sequences, respectively. The areas depicted are not proportional to the actual gene numbers, and the number of A. thaliana genes in each category is written in each segment.