title: 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.
authors.affiliation: Division of Speciation Mechanisms 2 and Computer Laboratory, National Institute for Basic Biology, Okazaki 444-8585, Japan.
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Nishiyama
authors.forename: Tomomichi
authors.initials: T
authors.lastname: Fujita
authors.forename: Tadasu
authors.initials: T
authors.lastname: Shin-I
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
authors.forename: Hiroyo
authors.initials: H
authors.lastname: Nishide
authors.forename: Ikuo
authors.initials: I
authors.lastname: Uchiyama
authors.forename: Asako
authors.initials: A
authors.lastname: Kamiya
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kohara
authors.forename: Mitsuyasu
authors.initials: M
authors.lastname: Hasebe
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D019068:Bryopsida / Q000235:genetics*; D019070:Cell Lineage; D018076:DNA, Complementary / Q000378:metabolism; D019992:Databases as Topic; D020224:Expressed Sequence Tags; D015723:Gene Library; D018745:Genome, Plant; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger