title: ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales).
abstract: BACKGROUND
  Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment.
  
  
  RESULTS
  The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae.
  
  
  CONCLUSIONS
  In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics.
authors.affiliation: Department of Bioinformatics, University of Würzburg, Am Hubland, 97074 Würzburg, Germany. a.keller@biozentrum.uni-wuerzburg.de
authors.forename: Alexander
authors.initials: A
authors.lastname: Keller
authors.forename: Tina
authors.initials: T
authors.lastname: Schleicher
authors.forename: Frank
authors.initials: F
authors.lastname: Förster
authors.forename: Benjamin
authors.initials: B
authors.lastname: Ruderisch
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.forename: Tobias
authors.initials: T
authors.lastname: Müller
authors.forename: Matthias
authors.initials: M
authors.lastname: Wolf
mesh_terms: D000818:Animals; D001483:Base Sequence; D002734:Chlorophyll / Q000502:physiology*; D000460:Chlorophyta / Q000145:classification* / Q000235:genetics*; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D019143:Evolution, Molecular; D005784:Gene Amplification; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D044444:Scenedesmus / Q000145:classification / Q000235:genetics
chemical_list: D021903:DNA, Ribosomal Spacer; D002734:Chlorophyll; D004247:DNA