title: Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny.
abstract: BACKGROUND
  Tunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctive features. Extensive gene rearrangements and particularly high evolutionary rates have been evidenced with regard to other chordates. This peculiar evolutionary dynamics has hampered the reconstruction of tunicate phylogenetic relationships within chordates based on mitogenomic data.
  
  
  RESULTS
  In order to further understand the atypical evolutionary dynamics of the mitochondrial genome of tunicates, we determined the complete sequence of the solitary ascidian Herdmania momus. This genome from a stolidobranch ascidian presents the typical tunicate gene content with 13 protein-coding genes, 2 rRNAs and 24 tRNAs which are all encoded on the same strand. However, it also presents a novel gene arrangement, highlighting the extreme plasticity of gene order observed in tunicate mitochondrial genomes. Probabilistic phylogenetic inferences were conducted on the concatenation of the 13 mitochondrial protein-coding genes from representatives of major metazoan phyla. We show that whereas standard homogeneous amino acid models support an artefactual sister position of tunicates relative to all other bilaterians, the CAT and CAT+BP site- and time-heterogeneous mixture models place tunicates as the sister-group of vertebrates within monophyletic chordates. Moreover, the reference phylogeny indicates that tunicate mitochondrial genomes have experienced a drastic acceleration in their evolutionary rate that equally affects protein-coding and ribosomal-RNA genes.
  
  
  CONCLUSIONS
  This is the first mitogenomic study supporting the new chordate phylogeny revealed by recent phylogenomic analyses. It illustrates the beneficial effects of an increased taxon sampling coupled with the use of more realistic amino acid substitution models for the reconstruction of animal phylogeny.
authors.affiliation: Department of Zoology, George S Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel.
authors.forename: Tiratha Raj
authors.initials: TR
authors.lastname: Singh
authors.forename: Georgia
authors.initials: G
authors.lastname: Tsagkogeorga
authors.forename: Frédéric
authors.initials: F
authors.lastname: Delsuc
authors.forename: Samuel
authors.initials: S
authors.lastname: Blanquart
authors.forename: Noa
authors.initials: N
authors.lastname: Shenkar
authors.forename: Yossi
authors.initials: Y
authors.lastname: Loya
authors.forename: Emmanuel Jp
authors.initials: EJ
authors.lastname: Douzery
authors.forename: Dorothée
authors.initials: D
authors.lastname: Huchon
mesh_terms: D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D023061:Gene Order; D054629:Genome, Mitochondrial / Q000235:genetics*; D023281:Genomics; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D014561:Urochordata / Q000166:cytology / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial; D012335:RNA, Ribosomal; D012343:RNA, Transfer