Article Mitochondrial Genome of Savalia savaglia (Cnidaria, Hexacorallia) and Early Metazoan Phylogeny SINNIGER, Frédéric, CHEVALDONNÉ, P., PAWLOWSKI, Jan Wojciech Abstract Mitochondrial genomes have recently become widely used in animal phylogeny, mainly to infer the relationships between vertebrates and other bilaterians. However, only 11 of 723 complete mitochondrial genomes available in the public databases are of early metazoans, including cnidarians (Anthozoa, mainly Scleractinia) and sponges. Although some cnidarians (Medusozoa) are known to possess atypical linear mitochondrial DNA, the anthozoan mitochondrial genome is circular and its organization is similar to that of other metazoans. Because the phylogenetic relationships among Anthozoa as well as their relation to other early metazoans still need to be clarified, we tested whether sequencing the complete mitochondrial genome of Savalia savaglia, an anthozoan belonging to the order Zoantharia (=Zoanthidea), could be useful to infer such relationships. Compared to other anthozoans, S. savaglia’s genome is unusually long (20,766 bp) due to the presence of several noncoding intergenic regions (3691 bp). The genome contains all 13 protein coding genes commonly found in metazoans, but like other Anthozoa it lacks most of the tRNAs. [...] Reference SINNIGER, Frédéric, CHEVALDONNÉ, P., PAWLOWSKI, Jan Wojciech. Mitochondrial Genome of Savalia savaglia (Cnidaria, Hexacorallia) and Early Metazoan Phylogeny. Journal of Molecular Evolution, 2007, vol. 64, no. 2, p. 196-203 DOI : 10.1007/s00239-006-0015-0 Available at: http://archive-ouverte.unige.ch/unige:117868 Disclaimer: layout of this document may differ from the published version. 1 / 1 J Mol Evol (2007) 64:196–203 DOI: 10.1007/s00239-006-0015-0 Mitochondrial Genome of Savalia savaglia (Cnidaria, Hexacorallia) and Early Metazoan Phylogeny F. Sinniger,1,2 P. Chevaldonne´,2 J. Pawlowski1 1 Department of Zoology and Animal Biology, Molecular Systematic Group, Science III, University of Geneva, 30 quai Ernest-Ansermet, 1211 Gene` ve 4, Switzerland 2 Centre d’Oce´anologie de Marseille, UMR CNRS 6540 DIMAR, Universite´de la Me´diterrane´e, Station Marine d’Endoume, rue de la Batterie des Lions, 13007 Marseille, France Received: 23 January 2006 / Accepted: 24 October 2006 [Reviewing Editor: Dr. Axel Meyer] Abstract. Mitochondrial genomes have recently tionships suggested between Zoantharia and Actin- become widely used in animal phylogeny, mainly to iaria are reinforced by strong similarities in their gene infer the relationships between vertebrates and other order and the presence of similar introns in the COI bilaterians. However, only 11 of 723 complete mito- and ND5 genes. Our study suggests that mitochon- chondrial genomes available in the public databases drial genomes can be a source of potentially valuable are of early metazoans, including cnidarians (An- information on the phylogeny of Hexacorallia and thozoa, mainly Scleractinia) and sponges. Although may provide new insights into the evolution of early some cnidarians (Medusozoa) are known to possess metazoans. atypical linear mitochondrial DNA, the anthozoan mitochondrial genome is circular and its organization Key words: Mitochondrial genome — Early meta- is similar to that of other metazoans. Because the zoan — Cnidaria — Anthozoa — Hexacorallia — phylogenetic relationships among Anthozoa as well Zoantharia as their relation to other early metazoans still need to be clarified, we tested whether sequencing the com- plete mitochondrial genome of Savalia savaglia,an anthozoan belonging to the order Zoantharia (=Zoanthidea), could be useful to infer such rela- Introduction tionships. Compared to other anthozoans, S. sava- glia’s genome is unusually long (20,766 bp) due to the Mitochondrial genomes are commonly used to infer presence of several noncoding intergenic regions metazoan phylogeny, their haploid status and their (3691 bp). The genome contains all 13 protein coding small size being the most important advantages as genes commonly found in metazoans, but like other phylogenetic markers. Seven hundred twenty-three Anthozoa it lacks most of the tRNAs. Phylogenetic complete mitochondrial genomes are available in the analyses of S. savaglia mitochondrial sequences show public databases (GenBank, January 2006) and this Zoantharia branching closely to other Hexacorallia, number is rapidly increasing. DNA sequences of either as a sister group to Actiniaria or as a sister tRNA, rRNA, and protein coding genes and inferred group to Actiniaria and Scleractinia. The close rela- amino acid sequences of protein coding genes as well as gene order provide different types of information useful at different taxonomic levels (Boore 1999). If Correspondence to: F. Sinniger; email: frederic.sinniger@zoo. mitochondrial DNA sequences are widely used for unige.ch species identification (Herbert et al. 2004; Ward et al. 197 2005) and for inferring relationships below the family been extensively used in cnidarian phylogeny but do level, rearrangements in gene order are mainly not provide much information at the species level informative for relationships between phyla (Jennings (Romano and Palumbi 1997; Sanchez et al. 2003; and Halanych 2005). However, such rearrangements Sinniger et al. 2005). Among Octocorallia the effi- have in some cases also been used to infer phylogeny ciency of mitochondrial markers is limited to the within phyla (Dreyer and Steiner 2004) and even genus level (McFadden et al. 2004) despite msh1 and within families (Mabuchi et al. 2004). some ND subunits being more variable and useful in Among the metazoan mitochondrial genomes se- solving phylogeny within suborders (Sanchez et al. quenced up until now, only 11 come from diploblastic 2004). organisms. Three of these mitochondrial genomes To increase taxon sampling of cnidarian mito- belong to demosponges: Tethya actinia, Geodia nep- chondrial genomes and to test their possible interest tuni (Lavrov et al. 2005), and Axinella corrugata for phylogenetic use, here we have sequenced the (Lavrov and Lang 2005). The other genomes belong complete mitochondrial genome of Savalia savaglia,a to anthozoans (Cnidaria), including the soft coral species belonging to the hexacorallian order Zoan- Sarcophyton glaucum (Octocorallia, Alcyonaria) tharia (=Zoanthidea, Zoanthiniaria). Phylogenetic (Beaton et al. 1998), the sea anemone Metridium se- analyses of obtained sequences confirm the mono- nile (Hexacorallia, Actiniaria) (Beagley et al. 1998), phyly of Hexacorallia and give insights into the and the six hard corals (Hexacorallia, Scleractinia). relationships among three orders (of a total of six) The scleratinian genomes include three species (Zoantharia, Actiniaria, Scleractinia) belonging to belonging to the family Acroporidae—Acropora ten- this class. In view of our data, the gene rearrange- uis (Van Oppen et al. 2002), Anacropora matthai, and ments in mitochondrial genomes provide important Montipora cactus (Tseng et al. 2005)—and three phylogenetic information at this taxonomic level. others belonging to the Montastrea annularis species complex (Fukami and Knowlton 2005). In addition to completely sequenced mitochondrial genomes, Materials and Methods there is also information on the order of genes in the mitochondrial genome of Renilla kollikeri (Octocor- Sampling and DNA Extraction allia, Pennatulacea) (Beagley et al. 1995) and Savalia savaglia (formerly in the genus Gerardia) was collected regarding the organization of the genome in Acropora from a colony originating from the Embiez Islands (France) and nasuta (Fukami et al. 2000). All these data show that, artificially implanted and reproduced on a small island off Mar- in opposition to Hydrozoa and other Medusozoa, seille (France). It is the only zoantharian (=zoanthid) genus to which possess linear mitochondrial genomes in one or secrete its own skeleton covering the substrate (usually gorgonians more parts (Bridge et al. 1992), all anthozoans se- or antipatharians). S. savaglia is found in the Mediterranean Sea at depths ranging from 30 to more than 100 m. The tissues were fixed quenced so far have circular mitochondrial genomes and conserved in 70% ethanol and two DNA extractions were like other metazoans. performed using the DNeasy Plant Minikit (Qiagen). To avoid The acquisition of the first complete mitochondrial contamination from epizoic organisms, DNA was extracted from a genomes of cnidarians and sponges prompted inves- fragment of mesenteria carefully isolated under the microscope. tigation of the utility of their use in inferring early Genomic DNA obtained was used to perform PCR amplifications. The absence of contamination was confirmed by sequence analyses, metazoan phylogeny. Until recently, the phylogenetic as none of the sequences obtained were similar to any potential study of the diploblastic taxa at higher taxonomic prey, parasite, epibiont, or other cnidarian species present in the levels was based mostly on the sequences of 28S and area. Moreover, the overlap between new sequences and previously 18S rDNA (Medina et al. 2001; Collins 2002; Bor- obtained zoantharian sequences (COI, 12S, 16S) warranted the chiellini et al. 2004). Despite such studies, different homogeneity of genomic material. phylogenetic questions concerning the relationships between diploblasts and bilaterians and relationships PCR Amplification and Sequencing within different diploblastic taxa remain partially or completely unanswered. Relationships at the base of PCR conditions were as