title: Organellar genomes of the four-toothed moss, Tetraphis pellucida.
abstract: BACKGROUND
  Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systematics is the branching order of these peristomate clades. Organellar genome sequencing offers the potential to resolve this issue through the provision of both genomic structural characters and a greatly increased quantity of nucleotide substitution characters, as well as to elucidate organellar evolution in mosses. We publish and describe the chloroplast and mitochondrial genomes of Tetraphis pellucida, representative of the most phylogenetically intractable and morphologically isolated peristomate lineage.
  
  
  RESULTS
  Assembly of reads from Illumina SBS and Pacific Biosciences RS sequencing reveals that the Tetraphis chloroplast genome comprises 127,489 bp and the mitochondrial genome 107,730 bp. Although genomic structures are similar to those of the small number of other known moss organellar genomes, the chloroplast lacks the petN gene (in common with Tortula ruralis) and the mitochondrion has only a non-functional pseudogenised remnant of nad7 (uniquely amongst known moss chondromes).
  
  
  CONCLUSIONS
  Structural genomic features exist with the potential to be informative for phylogenetic relationships amongst the peristomate moss lineages, and thus organellar genome sequences are urgently required for exemplars from other clades. The unique genomic and morphological features of Tetraphis confirm its importance for resolving one of the major questions in land plant phylogeny and for understanding the evolution of the peristome, a likely key innovation underlying the diversity of mosses. The functional loss of nad7 from the chondrome is now shown to have occurred independently in all three bryophyte clades as well as in the early-diverging tracheophyte Huperzia squarrosa.
authors.affiliation: Botanical Museum, Finnish Museum of Natural History, University of Helsinki, PO Box 7, FI-00014 Helsinki, Finland. neil.bell@helsinki.fi.
authors.forename: Neil E
authors.initials: NE
authors.lastname: Bell
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Boore
authors.forename: Brent D
authors.initials: BD
authors.lastname: Mishler
authors.forename: Jaakko
authors.initials: J
authors.lastname: Hyvönen
mesh_terms: D001483:Base Sequence; D044002:Bryophyta / Q000145:classification / Q000235:genetics*; D002874:Chromosome Mapping; D054628:Genome, Chloroplast; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D017423:Sequence Analysis, RNA