title: Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta).
abstract: OBJECTIVE
  The recent assembly of the complete sequence of the plastid genome of the model taxon Physcomitrella patens (Funariaceae, Bryophyta) revealed that a 71-kb fragment, encompassing much of the large single copy region, is inverted. This inversion of 57% of the genome is the largest rearrangement detected in the plastid genomes of plants to date. Although initially considered diagnostic of Physcomitrella patens, the inversion was recently shown to characterize the plastid genome of two species from related genera within Funariaceae, but was lacking in another member of Funariidae. The phylogenetic significance of the inversion has remained ambiguous.
  
  
  METHODS
  Exemplars of all families included in Funariidae were surveyed. DNA sequences spanning the inversion break ends were amplified, using primers that anneal to genes on either side of the putative end points of the inversion. Primer combinations were designed to yield a product for either the inverted or the non-inverted architecture.
  
  
  RESULTS
  The survey reveals that exemplars of eight genera of Funariaceae, the sole species of Disceliaceae and three generic representatives of Encalyptales all share the 71-kb inversion in the large single copy of the plastid genome. By contrast, the plastid genome of Gigaspermaceae (Funariales) is characterized by a gene order congruent with that described for other mosses, liverworts and hornworts, and hence it does not possess this inversion.
  
  
  CONCLUSIONS
  The phylogenetic distribution of the inversion in the gene order supports a hypothesis only weakly supported by inferences from sequence data whereby Funariales are paraphyletic, with Funariaceae and Disceliaceae sharing a common ancestor with Encalyptales, and Gigaspermaceae sister to this combined clade. To reflect these relationships, Gigaspermaceae are excluded from Funariales and accommodated in their own order, Gigaspermales order nov., within Funariideae.
authors.affiliation: Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, University of Connecticut, Storrs, CT 06269-3043, USA. bernard.goffinet@uconn.edu
authors.forename: Bernard
authors.initials: B
authors.lastname: Goffinet
authors.forename: Norman J
authors.initials: NJ
authors.lastname: Wickett
authors.forename: Olaf
authors.initials: O
authors.lastname: Werner
authors.forename: Rosa Maria
authors.initials: RM
authors.lastname: Ros
authors.forename: A Jonathan
authors.initials: AJ
authors.lastname: Shaw
authors.forename: Cymon J
authors.initials: CJ
authors.lastname: Cox
mesh_terms: D044002:Bryophyta / Q000145:classification* / Q000235:genetics; D007446:Chromosome Inversion; D023061:Gene Order; D018745:Genome, Plant; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D017422:Sequence Analysis, DNA