The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants

Abstract

It is generally believed that bryophytes are the earliest land plants. However, the phylogenetic relationships among bryophytes, including mosses, liverworts and hornworts, are not clearly resolved. To obtain more information on the earliest land plants, we determined the complete nucleotide sequence of the chloroplast genome from the hornwort Anthoceros formosae. The circular double-stranded DNA of 161 162 bp is the largest genome ever reported among land plant chloroplasts. It contains 76 protein, 32 tRNA and 4 rRNA genes and 10 open reading frames (ORFs), which are identical with the chloroplast genome of the other green plants analyzed. The major difference is a larger inverted repeat than that of the liverwort Marchantia, Anthoceros contains an excess of ndhB and rps7 genes and the 3' exon of rps12. The genes matK and rps15, commonly found in the chloroplast genomes of land plants, are pseudogenes. The intron of rrn23 is the first finding in the known chloroplast genomes of land plants. A striking feature of the hornwort chloroplast is that more than half of the protein-coding genes have nonsense codons, which are converted into sense codons by RNA editing. Maximum-likelihood (ML) analysis, based on 11 518 amino acid sites of 52 proteins encoded in the chloroplast genomes of the green plants, placed liverworts as the sister to all other land plants.

Phylogenetic significance of the rpoA loss in the chloroplast genome of mosses

“…The rps16 gene is lacking from the Marchantia genome, and has been lost from the plastid at least four times in the evolution of green plants (Martin & al., 2002). The genome of Anthoceros formosae is characterized by the presence of pseudogenes for matK and rps15 (Kugita & al., 2003). The structure of its inverted repeat is similar to that of vascular plants since it includes the rps12 gene (or only the 3' exon, according to Kugita & al.…”

The dynamic history of plastid genomes in the Campanulaceae sensu lato is unique among angiosperms

“…The IR copies recombine with sufficient frequency to maintain equimolar isomers in which the single-copy regions are inverted relative to one another (6,7), but the IR also confers stability to the remaining plastome organization (8). The land plant ancestral organization is readily inferred because the plastomes of the liverwort Marchantia polymorpha (9), the moss Syntrichia ruralis (10), the hornwort Anthoceros formosae (11), and the lycophyte Huperzia lucidula (12) are syntenic (they maintain parallel gene content and organization). The remaining land plants (euphyllophytes) share a 30-kb inversion in the LSC, and the resulting gene order is preserved in gymnosperms (such as Cycas taitungensis and Ginkgo biloba) and most angiosperms (except for lineage-specific gene losses and changes in the IR boundaries) (13)(14)(15)(16).…”

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

“…Marchantia polymorpha share the lack of petN in the cpDNA with some mosses, exceptly with P. patens. This species has the mitochondrial nad7 as a pseudogene; Anthoceros formosae Steph [29] has maturase K and rps15 as pseudogenes, characterizing these two pseudogenes in cpDNA of Anthocerotophyta [30]. In addition, nad7 from T. pellucida is considered a pseudogene [8].…”