TY - JOUR
T1 - Tunicate mitogenomics and phylogenetics
T2 - Peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny
AU - Singh, Tiratha R.
AU - Tsagkogeorga, Georgia
AU - Delsuc, Frédéric
AU - Blanquart, Samuel
AU - Shenkar, Noa
AU - Loya, Yossi
AU - Douzery, Emmanuel J.P.
AU - Huchon, Dorothée
N1 - Funding Information:
We would like to thank Tamar Feldstein and Isadora Cohen for their help at the bench, Benoît Nabholz for sharing scripts, two anonymous reviewers for their comments, and Naomi Paz for editing the text. TRS was supported by a fellowship from the Israel National Committee for Planning and Budgeting Universities (VATAT). This work has been funded by the Research Networks Program in BIOINFORMATICS of the High Council for Scientific and Technological Cooperation between France and Israel to DH, EJPD and YL, and have benefited from the ISE-M bioinformatics cluster. This publication is contribution N° 2009-109 of the Institut des Sciences de l'Evolution de Montpellier (UMR 5554 - CNRS).
PY - 2009/11/17
Y1 - 2009/11/17
N2 - 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. Conclusion: 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.
AB - 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. Conclusion: 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.
UR - http://www.scopus.com/inward/record.url?scp=71549149673&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-10-534
DO - 10.1186/1471-2164-10-534
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AN - SCOPUS:71549149673
SN - 1471-2164
VL - 10
JO - BMC Genomics
JF - BMC Genomics
M1 - 534
ER -