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Breton S. Comparative mitogenomics of Brachiopods reveals conservatism in articulate species and unusualness in inarticulate species. Mol Biol Rep 2024; 51:298. [PMID: 38341808 DOI: 10.1007/s11033-024-09270-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Brachiopods are a phylum of marine invertebrates with over 10,000 fossil species. Today, there are fewer than 500 extant species assigned to the class Articulata or Inarticulata and for which knowledge of evolutionary genetics and genomics is still poor. Until now, complete mitogenome sequences of two inarticulate species and four articulate species were available. METHODS AND RESULTS The complete mitogenome of the inarticulate brachiopod species Lingula reevii (20,778 bp) was obtained by using next generation sequencing. It contains 12 protein-coding genes (the annotation of atp8 is unsure), two ribosomal RNA genes, 26 transfer RNA genes, and one supernumerary ORF that is also conserved in the inarticulate species Lingula anatina. It is hypothesized that this ORF could represent a Lingula-specific mtORFan gene (without obvious homology to other genes). Comparative mitogenomics indicate the mitochondrial gene order of L. reevii is unique among brachiopods, and that compared to articulate species, inarticulate species exhibit massive mitogenome rearrangements, deviant ATP8 protein sequences and supernumerary ORFs, possibly representing species- or lineage-specific mtORFan genes. CONCLUSION The results of this study enrich genetics knowledge of extant brachiopods, which may eventually help to test hypotheses about their decline.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada.
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2
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Aydemir MN, Aydemir HB, Budak M, Kızıltepe B, Çelebi MŞ, Korkmaz EM, Başıbüyük HH. A novel, conserved and possibly functional motif "WHWGHTW" in mitochondrial transcription across Bilateria. Mitochondrion 2023; 68:72-80. [PMID: 36400160 DOI: 10.1016/j.mito.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/22/2022] [Accepted: 11/05/2022] [Indexed: 11/17/2022]
Abstract
The animal mitogenomes which undergone a reductive evolution has an obvious loss of coding capacity compared to their known closest relatives, but it has not yet been fully investigated why and how the intergenic regions do not encode protein and have no known functions, are stably maintained, replicated, and transmitted by the genome. These relatively small intergenic regions may not be under neutral evolution and they may have functional and/or regulatory roles that have yet to be identified. Here, the distribution pattern, sequence content and location of a novel sequence motif of 'WWWGHTW' were bioinformatically investigated and characterised by constructing a sampling mitogenome dataset of 1889 species from 14 phyla representing the clade of Bilateria. This motif is reverse complementary of the previously described DmTTF binding sequence and found in the nd4L- (X) -trnT gene cluster. This cluster commonly exhibits a strand displacement region and an intergenic region among the bilaterian superphylums, particularly in Ecdysozoa. This motif may be accepted as a substrate providing binding sites for the specific interaction with transcription factors because of (i) its reverse complementarity of previously described DmTTF binding sequence, and (ii) the possession of G and T nucleotides in the fourth and sixth positions, (iii) the bias on T and G nucleotides instead of C and A in the degenerated positions. This suggestion is also supported by the presence of a strand displacement region in the nd4L- (X) -trnT gene cluster, particularly in Ecdysozoa consisting of the most rearranged mitogenomes among the bilaterian superphylums.
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Affiliation(s)
- Merve Nur Aydemir
- Tokat Gaziosmanpaşa University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 60250 Tokat, Turkey.
| | - Habeş Bilal Aydemir
- Tokat Gaziosmanpaşa University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 60250 Tokat, Turkey
| | - Mahir Budak
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, 58140 Sivas, Turkey
| | - Birsel Kızıltepe
- Sivas Cumhuriyet University, Graduate School of Natural and Applied Sciences, Department of Bioinformatics, 58140 Sivas, Turkey
| | - Melissa Şafak Çelebi
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, 58140 Sivas, Turkey
| | - Ertan Mahir Korkmaz
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, 58140 Sivas, Turkey
| | - Hasan Hüseyin Başıbüyük
- Akdeniz University, Faculty of Health Sciences, Department of Gerontology, 07070 Antalya, Turkey
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3
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Schultz DT, Eizenga JM, Corbett-Detig RB, Francis WR, Christianson LM, Haddock SH. Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii. PeerJ 2020; 8:e8356. [PMID: 32025367 PMCID: PMC6991124 DOI: 10.7717/peerj.8356] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 12/04/2019] [Indexed: 11/20/2022] Open
Abstract
To date, five ctenophore species' mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.
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Affiliation(s)
- Darrin T. Schultz
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Jordan M. Eizenga
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Warren R. Francis
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Steven H.D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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4
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Hogan RI, Hopkins K, Wheeler AJ, Allcock AL, Yesson C. Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia). Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:764-777. [PMID: 31317811 DOI: 10.1080/24701394.2019.1634699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well as one species of the epi- and mesobenthic genus Virgularia. Seventeen circular genomes ranged from 18,513 bp (Halipteris cf. finmarchica) to 19,171 bp (Distichoptilum gracile) and contained all genes standard to octocoral mitochondrial genomes (14 protein-coding genes, two ribosomal RNA genes and one transfer RNA). We found at least three different gene orders in Pennatulacea: the ancestral gene order, the gene order found in bamboo corals (Family Isididae), and a novel gene order. The mitogenome of one species of Umbellula has a bipartite genome (∼13 kbp and ∼5 kbp), with good evidence that both parts are circular.
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Affiliation(s)
- Raissa I Hogan
- Department of Zoology, Ryan Institute, National University of Ireland , Galway , Ireland
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, Regent's Park , London , UK
| | - Andrew J Wheeler
- School of Biological, Earth and Environmental Sciences/iCRAG/ERI, University College Cork , Cork , Ireland
| | - A Louise Allcock
- Department of Zoology, Ryan Institute, National University of Ireland , Galway , Ireland
| | - Chris Yesson
- Institute of Zoology, Zoological Society of London, Regent's Park , London , UK
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Stampar SN, Broe MB, Macrander J, Reitzel AM, Brugler MR, Daly M. Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia. Sci Rep 2019; 9:6094. [PMID: 30988357 PMCID: PMC6465557 DOI: 10.1038/s41598-019-42621-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/04/2019] [Indexed: 01/10/2023] Open
Abstract
Sequences and structural attributes of mitochondrial genomes have played a critical role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia (“tube anemones”) remains one of the most enigmatic in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both Isarachnanthus nocturnus and Pachycerianthus magnus, the mitochondrial gene sequences could not be assembled into a single circular genome. Instead, our analyses suggest that both species have mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The inferred number of fragments and variation in gene order between species is much greater within Ceriantharia than among the lineages of Medusozoa. We identify origins of replication for each of the five putative chromosomes of the Isarachnanthus nocturnus mitogenome and for each of the eight putative chromosomes of the Pachycerianthus magnus mitogenome. At 80,923 bp, I. nocturnus now holds the record for the largest animal mitochondrial genome reported to date. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other Anthozoa. The presence of tRNAMet and tRNATrp in both ceriantharian mitogenomes supports a closer relationship between Ceriantharia and Hexacorallia than between Ceriantharia and any other cnidarian lineage, but phylogenetic analysis of the genes contained in the mitogenomes suggests that Ceriantharia is sister to a clade containing Octocorallia + Hexacorallia indicating a possible suppression of tRNATrp in Octocorallia.
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Affiliation(s)
- Sérgio N Stampar
- Departamento de Ciências Biológicas, Faculdade de Ciências e Letras, UNESP - Universidade Estadual Paulista, Assis, SP, Brazil.
| | - Michael B Broe
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Jason Macrander
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Department of Biology, Florida Southern College, Lakeland, FL, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mercer R Brugler
- Biological Sciences Department, NYC College of Technology, City University of New York, 285 Jay Street, Brooklyn, New York, 11201, USA.,Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, USA
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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6
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Poliseno A, Feregrino C, Sartoretto S, Aurelle D, Wörheide G, McFadden CS, Vargas S. Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae). Mol Phylogenet Evol 2017; 115:181-189. [PMID: 28782594 DOI: 10.1016/j.ympev.2017.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/05/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
Abstract
Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms.
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Affiliation(s)
- Angelo Poliseno
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany.
| | - Christian Feregrino
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany.
| | - Stéphane Sartoretto
- IFREMER, Z.P: de Brègaillon, CS 20330, 83507 La Seyne-sur-mer Cedex, France.
| | - Didier Aurelle
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, 13007 Marseille, France.
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany; Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333 München, Germany.
| | | | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany.
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7
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Abstract
BACKGROUND Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. RESULTS We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, the mtMutS, was found to undergo alternative polyadenylation, and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected. CONCLUSIONS Mt-mRNA processing in octocorals possessing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represent a first step towards understanding its functional and evolutionary implications.
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8
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Historical biogeography and mitogenomics of two endemic Mediterranean gorgonians (Holaxonia, Plexauridae). ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-017-0322-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Breton S, Milani L, Ghiselli F, Guerra D, Stewart DT, Passamonti M. A resourceful genome: updating the functional repertoire and evolutionary role of animal mitochondrial DNAs. Trends Genet 2014; 30:555-64. [PMID: 25263762 DOI: 10.1016/j.tig.2014.09.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 11/24/2022]
Abstract
Recent data from mitochondrial genomics and proteomics research demonstrate the existence of several atypical mitochondrial protein-coding genes (other than the standard set of 13) and the involvement of mtDNA-encoded proteins in functions other than energy production in several animal species including humans. These results are of considerable importance for evolutionary and cellular biology because they indicate that animal mtDNAs have a larger functional repertoire than previously believed. This review summarizes recent studies on animal species with a non-standard mitochondrial functional repertoire and discusses how these genetic novelties represent promising candidates for studying the role of the mitochondrial genome in speciation.
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Affiliation(s)
- Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, 90 Avenue Vincent d'Indy, Montréal, Québec H2V 2S9, Canada.
| | - Liliana Milani
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Fabrizio Ghiselli
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Davide Guerra
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Donald T Stewart
- Department of Biology, Acadia University, 24 University Avenue, Wolfville, Nova Scotia B4P 2R6, Canada
| | - Marco Passamonti
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
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10
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Kitahara MV, Lin MF, Forêt S, Huttley G, Miller DJ, Chen CA. The "naked coral" hypothesis revisited--evidence for and against scleractinian monophyly. PLoS One 2014; 9:e94774. [PMID: 24740380 PMCID: PMC3989238 DOI: 10.1371/journal.pone.0094774] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 03/20/2014] [Indexed: 12/01/2022] Open
Abstract
The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are “naked corals” that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the “naked coral” hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. The initial observation was that, whereas analyses based on nt data support scleractinian monophyly, those based on amino acid (aa) data support the “naked coral” hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of “Robust” corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the “naked coral” topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. The equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data.
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MESH Headings
- Amino Acids/genetics
- Animals
- Anthozoa/classification
- Anthozoa/genetics
- Base Composition/genetics
- Codon/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- Genome, Mitochondrial/genetics
- Mitochondrial Proteins/genetics
- Phylogeny
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Transfer, Met/genetics
- RNA, Transfer, Trp/genetics
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Marcelo V. Kitahara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
- Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - Mei-Fang Lin
- School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
- Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gavin Huttley
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - David J. Miller
- School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- * E-mail: (CAC); (DJM)
| | - Chaolun Allen Chen
- Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Taipei, Taiwan
- * E-mail: (CAC); (DJM)
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Osigus HJ, Eitel M, Bernt M, Donath A, Schierwater B. Mitogenomics at the base of Metazoa. Mol Phylogenet Evol 2013; 69:339-51. [PMID: 23891951 DOI: 10.1016/j.ympev.2013.07.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/29/2013] [Accepted: 07/09/2013] [Indexed: 11/25/2022]
Abstract
Unraveling the base of metazoan evolution is of crucial importance for rooting the metazoan Tree of Life. This subject has attracted substantial attention for more than a century and recently fueled a burst of modern phylogenetic studies. Conflicting scenarios from different studies and incongruent results from nuclear versus mitochondrial markers challenge current molecular phylogenetic approaches. Here we analyze the presently most comprehensive data sets of mitochondrial genomes from non-bilaterian animals to illuminate the phylogenetic relationships among early branching metazoan phyla. The results of our analyses illustrate the value of mitogenomics and support previously known topologies between animal phyla but also identify several problematic taxa, which are sensitive to long branch artifacts or missing data.
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Affiliation(s)
- Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology and Evolution, Buenteweg 17d, D-30559 Hannover, Germany.
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12
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Pante E, Saucier EH, France SC. Molecular and morphological data support reclassification of the octocoral genus Isidoides. INVERTEBR SYST 2013. [DOI: 10.1071/is12053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The rare octocoral genus Isidoides Nutting, 1910 was originally placed in the Gorgonellidae (now the Ellisellidae), even though it showed a remarkable similarity to the Isidae (now the Isididae). Isidoides was not classified in the Isididae mostly because the type specimen lacked skeletal nodes, a defining characteristic of that family. The genus was later assigned to the Chrysogorgiidae based on sclerite morphology. Specimens were recently collected in the south-western Pacific, providing material for genetic analysis and detailed characterisation of the morphology, and allowing us to consider the systematic placement of this taxon within the suborder Calcaxonia. A previously reported phylogeny allowed us to reject monophyly with the Chrysogorgiidae, and infer a close relationship with the Isididae subfamily Keratoisidinae. While scanning for molecular variation across mitochondrial genes, we discovered a novel gene order that is, based on available data, unique among metazoans. Despite these new data, the systematic placement of Isidoides is still unclear, as (1) the phylogenetic relationships among Isididae subfamilies remain poorly resolved, (2) genetic distances between mitochondrial mtMutS sequences from Isidoides and Keratoisidinae are characteristic of intra-familial distances, and (3) mitochondrial gene rearrangements may occur among confamilial genera. For these reasons, and because a revision of the Isididae is beyond the scope of this contribution, we amend the familial placement of Isidoides to incertae sedis.
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13
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Brockman SA, McFadden CS. The mitochondrial genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports intramolecular recombination as the primary mechanism of gene rearrangement in octocoral mitochondrial genomes. Genome Biol Evol 2012; 4:994-1006. [PMID: 22975720 PMCID: PMC3468961 DOI: 10.1093/gbe/evs074] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene content and nucleotide composition are, however, identical to most other octocorals, and the additional length is due to the presence of two large, noncoding intergenic regions. Relative to the presumed ancestral octocoral gene order, in P. aldersladei a block of three protein-coding genes (nad6–nad3–nad4l) has been translocated and inverted. Mapping the distribution of mt gene arrangements onto a taxonomically comprehensive phylogeny of Octocorallia suggests that all of the known octocoral gene orders have evolved by successive inversions of one or more evolutionarily conserved blocks of protein-coding genes. This mode of genome evolution is unique among Metazoa, and contrasts strongly with that observed in Hexacorallia, in which extreme gene shuffling has occurred among taxonomic orders. Two of the four conserved gene blocks found in Octocorallia are, however, also conserved in the linear mt genomes of Medusozoa and in one group of Demospongiae. We speculate that the rate and mechanism of gene rearrangement in octocorals may be influenced by the presence in their mt genomes of mtMutS, a putatively active DNA mismatch repair protein that may also play a role in mediating intramolecular recombination.
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Xu X, Wu X, Yu Z. Comparative studies of the complete mitochondrial genomes of four Paphia clams and reconsideration of subgenus Neotapes (Bivalvia: Veneridae). Gene 2012; 494:17-23. [DOI: 10.1016/j.gene.2011.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 11/09/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
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Park E, Hwang DS, Lee JS, Song JI, Seo TK, Won YJ. Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. Mol Phylogenet Evol 2012; 62:329-45. [DOI: 10.1016/j.ympev.2011.10.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 10/01/2011] [Accepted: 10/04/2011] [Indexed: 01/18/2023]
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Kayal E, Bentlage B, Collins AG, Kayal M, Pirro S, Lavrov DV. Evolution of linear mitochondrial genomes in medusozoan cnidarians. Genome Biol Evol 2011; 4:1-12. [PMID: 22113796 PMCID: PMC3267393 DOI: 10.1093/gbe/evr123] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans.
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Affiliation(s)
- Ehsan Kayal
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, USA.
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