title: The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain.
abstract: OBJECTIVE
  The previously sequenced plastome of the hornwort Anthoceros angustus differs from that of other bryophytes by an expanded inverted repeat (IR) and the presence of a type I intron in the 23S ribosomal RNA (rrn23) gene. We assembled the plastome of the hornwort Nothoceros aenigmaticus, contrasted its architecture to that of other bryophytes, and assessed the phylogenetic significance of genomic characters in hornwort evolution. •
  
  
  METHODS
  The Nothoceros plastome was reconstructed from shotgun sequencing of genomic DNA. Comparison with the Anthoceros plastome revealed three structural differences. We sequenced these regions in taxa spanning the hornwort phylogeny. •
  
  
  RESULTS
  The Nothoceros plastome is colinear with other bryophyte plastomes, but differs from the Anthoceros plastome by several gene regions located within the IR in Anthoceros being in the large single-copy region in Nothoceros, by the rrn23 gene lacking an intron, and by the rpl2 being a pseudogene. Comparisons across the hornwort phylogeny indicate that the first two characters are restricted to Anthocerotaceae, while rpl2 pseudogenization diagnoses the sister lineage to Anthocerotaceae. •
  
  
  CONCLUSIONS
  The Nothoceros plastome is structurally similar to that of most bryophytes. However, we identified more structural differences within hornworts than have been described within either the mosses or the liverworts. The distribution of the gene duplication involving the IR and an intron in the rrn23 gene are restricted to Anthocerotaceae. Occurrence of the intron and the conserved intron sequence between Anthoceros and distantly related chlorophyte algae may be due to horizontal gene transfer.
authors: Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, University of Connecticut, Storrs, CT 06269-3043, USA. jcarlos.villarreal@gmail.com
authors: Juan Carlos
authors: JC
authors: Villarreal
authors: Laura Lowe
authors: LL
authors: Forrest
authors: Norman
authors: N
authors: Wickett
authors: Bernard
authors: B
authors: Goffinet
mesh_terms: D049936:Anthocerotophyta / Q000235:genetics*; D001483:Base Sequence; D017343:Genes, Plant / Q000235:genetics; D054627:Genome, Plastid / Q000235:genetics*; D007438:Introns / Q000235:genetics*; D055029:Inverted Repeat Sequences / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011544:Pseudogenes / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D010940:Plant Proteins