Comparative genomics ofPhyscomitrella patensgametophytic transcriptome andArabidopsis 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.

The MADS-domain protein PPM2 preferentially occurs in gametangia and sporophytes of the moss Physcomitrella patens

“…The fact that sporophyte-dominant plants evolved from gametophyte-dominant ancestors suggests that the precursors of land plant MADS-box genes, like the precursors of many other genes, originated from genes which were active in the haploid generation and were recruited into a functional context in the diploid phase during the evolution of land plants (Nishiyama et al, 2003;Kofuji et al, 2003;Tanabe et al, 2005). To verify this hypothesis, information on a number of informative non-seed plant lineages, which have been analyzed for their MADS-box gene families and the respective gene expression patterns, was collected and scrutinized.…”

Exploring the Plant Transcriptome through Phylogenetic Profiling

“…Monocotyledonous plants, such as Triticum aestivum, Zea mays, Sorghum bicolor, and Hordeum vulgare, are also well represented, as well as the eudicotyledonous plants Glycine max, Medicago truncatula, Solanum tuberosum, Lycopersicon esculentum, and Vitis vinifera. For the moss Physcomitrella patens, more than 6,300 proteins are clustered into gene families, which can be explained by the exhaustive EST-sequencing efforts lately (Nishiyama et al, 2003). By contrast, for other plants only a limited number of protein sequences are available.…”

Controlled Expression of Recombinant Proteins in Physcomitrella patens by a Conditional Heat-shock Promoter: a Tool for Plant Research and Biotechnology

“…Moreover, genetic studies in haploid mosses such as P. patens are much simpler than in diploid plants (Cove et al, 1997;Schaefer and Zryd, 2001). Molecular tools (Schaefer and Zryd, 2004) and genetic information (Rensing et al, 2002;Nishiyama et al, 2003) are rapidly developing for P. patens. However, one tool still in need to be developed is a versatile conditional gene-expression system allowing to generate conditional phenotypes and circumvent lethality in mutations of essential genes.…”