1
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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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Struck TH, Golombek A, Hoesel C, Dimitrov D, Elgetany AH. Mitochondrial Genome Evolution in Annelida-A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution. Syst Biol 2023; 72:925-945. [PMID: 37083277 PMCID: PMC10405356 DOI: 10.1093/sysbio/syad023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/22/2023] Open
Abstract
The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA, and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene order variability including, among others, increased substitution rates, base composition differences, structure of noncoding regions, parasitism, living in extreme habitats, short generation times, and biomineralization. However, these analyses were neither done systematically nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits, and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best-predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, variability of the gene order does not predict if a taxon is difficult to place in molecular phylogenetic reconstructions using sequence data or not. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why the canonical views do not always fit to the observed patterns without making some adjustments. [Annelida; compositional biases; ecology; gene order; life history; macroevolution; mitochondrial genomes; substitution rates.].
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Affiliation(s)
- Torsten H Struck
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
- Centre of Molecular Biodiversity Research, Zoological Research Museum Alexander KoenigBonn 53113, Germany
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Anja Golombek
- Centre of Molecular Biodiversity Research, Zoological Research Museum Alexander KoenigBonn 53113, Germany
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Christoph Hoesel
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
| | - Asmaa Haris Elgetany
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
- Zoology Department, Faculty of Science, Damietta University, New Damietta, Central zone, 34517, Egypt
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3
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Cejp B, Ravara A, Aguado MT. First mitochondrial genomes of Chrysopetalidae (Annelida) from shallow-water and deep-sea chemosynthetic environments. Gene 2022; 815:146159. [PMID: 34995739 DOI: 10.1016/j.gene.2021.146159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023]
Abstract
Among Annelida, Chrysopetalidae is an ecologically and morphologically diverse group, which includes shallow-water, deep-sea, free-living, and symbiotic species. Here, the four first mitochondrial genomes of this group are presented and described. One of the free-living shallow-water species Chrysopetalum debile (Chrysopetalinae), one of the yet undescribed free-living deep-sea species Boudemos sp., and those of the two deep-sea bivalve endosymbionts Craseoschema thyasiricola and Iheyomytilidicola lauensis (Calamyzinae). An updated phylogeny of Chrysopetalidae is performed, which supports previous phylogenetic hypotheses within Chrysopetalinae and indicates a complex ecological evolution within Calamyzinae. Additionally, analyses of natural selection pressure in the four mitochondrial genomes and additional genes from the two shallow-water species Bhawania goodei and Arichlidon gathofi were performed. Relaxed selection pressure in the mitochondrion of deep-sea and symbiotic species was found, with many sites under selection identified in the COX3 gene of deep-sea species.
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Affiliation(s)
- Benjamin Cejp
- Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, 37073, Germany.
| | - Ascensão Ravara
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
| | - M Teresa Aguado
- Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, 37073, Germany.
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4
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Goto R, Takano T, Seike K, Yamashita M, Paulay G, Rodgers KS, Hunter CL, Tongkerd P, Sato S, Hong JS, Endo K. Stasis and diversity in living fossils: species delimitation and evolution of lingulid brachiopods. Mol Phylogenet Evol 2022; 175:107460. [DOI: 10.1016/j.ympev.2022.107460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 10/18/2022]
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5
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Yang Q, Guo K, Zhou X, Tang X, Yu X, Yao W, Wu Z. Histopathology, antioxidant responses, transcriptome and gene expression analysis in triangle sail mussel Hyriopsis cumingii after bacterial infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 124:104175. [PMID: 34147569 DOI: 10.1016/j.dci.2021.104175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 05/26/2023]
Abstract
Bacterial disease outbreaks in filter feeder bivalve Hyriopsis cumingii as water contamination become more frequent in the water ecosystem, especially in intensive aquaculture habitats. To characterize host-pathogen interactions between H. cumingii and bacterial infection, we investigated the effects of Stenotrophomonas maltophilia HOP3 and Aeromonas veronii GL1 on the antioxidant response, tissue invasion and transcriptome expression of H. cumingii by infectivity trials. We showed that bacterial infections resulted in tubular necrosis of the hepatopancreas and induced the acute immune response in H. cumingii. The transcriptomic study identified a total of 5957 differentially expressed genes (DEGs) after A. veronii challenge. These DEGs were implicated in 302 KEGG pathways, notably in Apoptosis, Phagosome and Lysosome. The results showed that the relative expressions of all six immune-related DEGs were effectively stimulated with A. veronii, accompanied by tissue differences. Overall, these findings will contribute to an analysis of the immune response of H. cumingii to bacterial infection at the transcriptomic level and its genomic resource for research.
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Affiliation(s)
- Qinglin Yang
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center of Fishery Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Kefan Guo
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center of Fishery Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Xicheng Zhou
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center of Fishery Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Xiaoqi Tang
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center of Fishery Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Xiaobo Yu
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center of Fishery Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Weizhi Yao
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center of Fishery Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Zhengli Wu
- College of Fisheries, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Research Center of Fishery Resources and Environment, Southwest University, Chongqing, 400715, China.
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6
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Niaison T, Guerra D, Breton S. The complete mitogenome of the inarticulate brachiopod Glottidia pyramidata reveals insights into gene order variation, deviant ATP8 and mtORFans in the Brachiopoda. Mitochondrial DNA B Resour 2021; 6:2701-2703. [PMID: 34435125 PMCID: PMC8381911 DOI: 10.1080/23802359.2021.1966342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Brachiopods are a clade of marine organisms with a tremendously diverse and abundant fossil record but with fewer than 500 species extant today. Even if a better understanding of their biology and genetics could help to test hypotheses about their impressive decline, knowledge of genetics and evolutionary genomics in extant brachiopods is very poor. Here, we present the complete mitochondrial genome sequence of the inarticulate Glottidia pyramidata, an eastern North American extant representative of the phylum Brachiopoda. Besides the general characteristics of the sequenced mitogenome, we present its unusual features such as deviant ATP8 protein sequence and supernumerary ORFs, and also unique gene order, considering the available genome sequences of other brachiopod species.
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Affiliation(s)
- Thierry Niaison
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Davide Guerra
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
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7
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Karagozlu MZ, Do TD, Kim JI, Choi TJ, Kim SG, Kim CB. An Investigation of the Variations in Complete Mitochondrial Genomes of Lingula anatina in the Western Pacific Region. BIOLOGY 2021; 10:biology10050367. [PMID: 33922950 PMCID: PMC8146825 DOI: 10.3390/biology10050367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/04/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Lingula anatina is a brachiopod widely distributed in the western Pacific region. Even though L. anatina has been targeted for a number of biological studies, there is still limited information on intraspecific genetic variations of L. anatina. In this study, L. anatina specimens were collected from Korea and Vietnam, and complete mitochondrial genome (mitogenome) sequences were analyzed and compared with previous records. The total mitogenomes of L. anatina were 24,875 bp and 25,305 bp in size for Korean and Vietnamese specimens, respectively. Those mitogenomes are extraordinarily longer than the typical mitogenome size for an animal but shorter than the previous record from Yanagawa (Japan) for this species. The gene orders and the sizes of the protein-coding genes are also different from those for the Japanese specimen. Furthermore, the nonsynonymous (Ka) and synonymous (Ks) substitution rates in protein-coding genes (PCGs) were calculated to test the idea of evolutionary rate differences in mitochondrial genomes. The analyses showed relatively low Ka and Ks for the complete mitogenomes from Buan (Korea), Doson (Vietnam) and Yanagawa (Japan). The Ka/Ks ratio was less than 1 in comparisons of three localities, indicating the existence of purifying selection in this species. The phylogenetic analyses showed that L. anatina diverged among localities in the western Pacific region.
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Affiliation(s)
- Mustafa Zafer Karagozlu
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
- 3Billion Inc., Seoul 06193, Korea
| | - Thinh Dinh Do
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Haiphong 04000, Vietnam
| | - Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
| | - Tae-June Choi
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
| | - Seong-Geun Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
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8
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Ghiselli F, Gomes-Dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. Molluscan mitochondrial genomes break the rules. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200159. [PMID: 33813887 DOI: 10.1098/rstb.2020.0159] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - André Gomes-Dos-Santos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, and Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, USA
| | - Manuel Lopes-Lima
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Jeffrey L Boore
- Providence St Joseph Health and the Institute for Systems Biology, Seattle, USA
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9
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Kutyumov VA, Predeus AV, Starunov VV, Maltseva AL, Ostrovsky AN. Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features. Mitochondrion 2021; 59:96-104. [PMID: 33631347 DOI: 10.1016/j.mito.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022]
Abstract
Bryozoans are aquatic colonial suspension-feeders abundant in many marine and freshwater benthic communities. At the same time, the phylum is under studied on both morphological and molecular levels, and its position on the metazoan tree of life is still disputed. Bryozoa include the exclusively marine Stenolaemata, predominantly marine Gymnolaemata and exclusively freshwater Phylactolaemata. Here we report the mitochondrial genome of the phylactolaemate bryozoan Cristatella mucedo. This species has the largest (21,008 bp) of all currently known bryozoan mitogenomes, containing a typical metazoan gene compendium as well as a number of non-coding regions, three of which are longer than 1500 bp. The trnS1/trnG/nad3 region is presumably duplicated in this species. Comparative analysis of the gene order in C. mucedo and another phylactolaemate bryozoan, Pectinatella magnifica, confirmed their close relationships, and revealed a stronger similarity to mitogenomes of phoronids and other lophotrochozoan species than to marine bryozoans, indicating the ancestral nature of their gene arrangement. We suggest that the ancestral gene order underwent substantial changes in different bryozoan cladesshowing mosaic distribution of conservative gene blocks regardless of their phylogenetic position. Altogether, our results support the early divergence of Phylactolaemata from the rest of Bryozoa.
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Affiliation(s)
- Vladimir A Kutyumov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia.
| | - Alexander V Predeus
- Bioinformatics Institute, Kantemirovskaya 2A, 197342 Saint Petersburg, Russia
| | - Viktor V Starunov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Arina L Maltseva
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Andrew N Ostrovsky
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Department of Palaeontology, Faculty of Geography, Geology and Astronomy, University of Vienna, Althanstr. 14, 1090 Vienna, Austria.
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10
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Sun Y, Daffe G, Zhang Y, Pons J, Qiu JW, Kupriyanova EK. Another blow to the conserved gene order in Annelida: Evidence from mitochondrial genomes of the calcareous tubeworm genus Hydroides. Mol Phylogenet Evol 2021; 160:107124. [PMID: 33610649 DOI: 10.1016/j.ympev.2021.107124] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/15/2021] [Accepted: 02/11/2021] [Indexed: 01/07/2023]
Abstract
Mitochondrial genomes are frequently applied in phylogenetic and evolutionary studies across metazoans, yet they are still poorly represented in many groups of invertebrates, including annelids. Here, we report ten mitochondrial genomes from the annelid genus Hydroides (Serpulidae) and compare them with all available annelid mitogenomes. We detected all 13 protein coding genes in Hydroides spp., including the atp8 which was reported as a missing gene in the Christmas Tree worm Spirobranchus giganteus, another annelid of the family Serpulidae. All available mitochondrial genomes of Hydroides show a highly positive GC skew combined with a highly negative AT skew - a feature consistent with that found only in the mitogenome of S. giganteus. In addition, amino acid sequences of the 13 protein-coding genes showed a high genetic distance between the Hydroides clade and S. giganteus, suggesting a fast rate of mitochondrial sequence evolution in Serpulidae. The gene order of protein-coding genes within Hydroides exhibited extensive rearrangements at species level, and were different from the arrangement patterns of other annelids, including S. giganteus. Phylogenetic analyses based on protein-coding genes recovered Hydroides as a monophyletic group sister to Spirobranchus with a long branch, and sister to the fan worm Sabellidae. Yet the Serpulidae + Sabellidae clade was unexpectedly grouped with Sipuncula, suggesting that mitochondrial genomes alone are insufficient to resolve the phylogenetic position of Serpulidae within Annelida due to its high base substitution rates. Overall, our study revealed a high variability in the gene order arrangement of mitochondrial genomes within Serpulidae, provided evidence to question the conserved pattern of the mitochondrial gene order in Annelida and called for caution when applying mitochondrial genes to infer their phylogenetic relationships.
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Affiliation(s)
- Yanan Sun
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, 224 Waterloo Road, Hong Kong; Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia
| | - Guillemine Daffe
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; Universite de Bordeaux, CNRS, INRAE, La Rochelle Universite, UMS 2567 POREA, 33615 Pessac, France
| | - Yanjie Zhang
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, 224 Waterloo Road, Hong Kong
| | - Joan Pons
- Diversidad Animal y Microbiana, Instituto Mediterráneo de Estudios Avanzados IMEDEA (CSIC-UIB), Esporles, Balearic Islands, Spain
| | - Jian-Wen Qiu
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, 224 Waterloo Road, Hong Kong
| | - Elena K Kupriyanova
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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11
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Tempestini A, Massamba-N'Siala G, Vermandele F, Beaudreau N, Mortz M, Dufresne F, Calosi P. Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha. BMC Genomics 2020; 21:815. [PMID: 33225885 PMCID: PMC7682095 DOI: 10.1186/s12864-020-07176-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Annelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and families within the phylum Annelida are still represented by a single specimen of a single species. The genus of interstitial annelids Ophryotrocha (Dorvilleidae, Errantia, Annelida) is among these neglected groups, despite its extensive use as model organism in numerous studies on the evolution of life history, physiological and ecological traits. To compensate for the paucity of genomic information in this genus, we here obtained novel complete mitochondrial genomes of six Ophryotrocha species using next generation sequencing. In addition, we investigated the evolution of the reproductive mode in the Ophryotrocha genus using a phylogeny based on two mitochondrial markers (COXI and 16S rDNA) and one nuclear fragment (Histone H3). RESULTS Surprisingly, gene order was not conserved among the six Ophryotrocha species investigated, and varied greatly as compared to those found in other annelid species within the class Errantia. The mitogenome phylogeny for the six Ophryotrocha species displayed a separation of gonochoric and hermaphroditic species. However, this separation was not observed in the phylogeny based on the COX1, 16S rDNA, and H3 genes. Parsimony and Bayesian ancestral trait reconstruction indicated that gonochorism was the most parsimonious ancestral reproductive mode in Ophryotrocha spp. CONCLUSIONS Our results highlight the remarkably high level of gene order variation among congeneric species, even in annelids. This encourages the need for additional mitogenome sequencing of annelid taxa in order to properly understand its mtDNA evolution, high biodiversity and phylogenetic relationships.
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Affiliation(s)
- Astrid Tempestini
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Gloria Massamba-N'Siala
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Fanny Vermandele
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Nicholas Beaudreau
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Mathieu Mortz
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - France Dufresne
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Piero Calosi
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada.
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12
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Abstract
Lingulids and discinids are the only brachiopods that exhibit life histories that include a feeding planktonic stage usually referred to as a “larva”. We collected planktotrophic brachiopod larvae from the Pacific and Caribbean coasts of Panama and took a DNA barcoding approach with mitochondrial cytochrome c oxidase subunit I (COI), mitochondrial ribosomal 16S, and nuclear ribosomal 18S genes to identify those larvae and to estimate their diversity in the region. We observed specimens from both coasts with distinct morphologies typical of lingulid and discinid larvae. COI and 16S were sequenced successfully for the lingulid larvae but failed consistently for all discinid larvae. 18S was sequenced successfully for larvae from both families. Sequence data from each gene revealed one lingulid operational taxonomic unit (OTU) from Bocas del Toro on the Caribbean coast, and one lingulid OTU from the Bay of Panama on the Pacific coast. These OTUs differed by >20% for COI, >10% for 16S and ~0.5% for 18S. Both OTUs clustered with GenBank sequences of Glottidia species, the only genus of lingulids in the Americas, but were distinct from G. pyramidata the only species reported for the Caribbean. Analysis of 18S sequence data for discinid larvae recovered 2 OTUs, one exclusively from the Pacific and one with a mixture of Pacific and Caribbean larvae. The 18S marker does not provide enough resolution to distinguish between species, and comparisons with GenBank sequences suggest that one OTU includes Pelagodiscus species, while the other may include Discradisca species. When compared with other marine invertebrates, our surveys of brachiopod larvae through DNA barcoding show relatively low levels of diversity for Panama.
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Abstract
Biologists would be mistaken if they relegated living fossils to paleontological inquiry or assumed that the concept is dead. It is now used to describe entities ranging from viruses to higher taxa, despite recent warnings of misleading inferences. Current work on character evolution illustrates how analyzing living fossils and stasis in terms of parts (characters) and wholes (e.g., organisms and lineages) advances our understanding of prolonged stasis at many hierarchical levels. Instead of viewing the concept's task as categorizing living fossils, we show how its primary role is to mark out what is in need of explanation, accounting for the persistence of both molecular and morphological traits. Rethinking different conceptions of living fossils as specific hypotheses reveals novel avenues for research that integrate phylogenetics, ecological and evolutionary modeling, and evo-devo to produce a more unified theoretical outlook.
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Affiliation(s)
- Scott Lidgard
- Integrative Research Center, Field Museum, Chicago, Illinois
| | - Alan C Love
- Department of Philosophy and the Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis
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The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum. ACTA ACUST UNITED AC 2018; 4. [PMID: 30105092 DOI: 10.1017/pao.2018.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.
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15
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Guerra D, Bouvet K, Breton S. Mitochondrial gene order evolution in Mollusca: Inference of the ancestral state from the mtDNA of Chaetopleura apiculata (Polyplacophora, Chaetopleuridae). Mol Phylogenet Evol 2017; 120:233-239. [PMID: 29258879 DOI: 10.1016/j.ympev.2017.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 11/18/2017] [Accepted: 12/11/2017] [Indexed: 11/15/2022]
Abstract
The mitochondrial genome architecture of polyplacophorans has been usually regarded as being very ancient in comparison to all mollusks. However, even if some complete chiton mtDNAs have been recently sequenced, thorough studies of their evolution are lacking. To further expand the set of complete chiton mtDNAs and perform such analysis, we sequenced the mitochondrial genome of the Eastern beaded chiton Chaetopleura apiculata (Chaetopleuridae) using next-generation sequencing. With mitochondrial sequences from all available chiton mtDNAs, we also built a phylogeny on which we reconstructed the evolution of gene arrangement in this class. The arrangement of C. apiculata proved to be the most primitive known so far for polyplacophorans. Comparing this gene order to those of other molluscan classes, we found that it most probably is the original gene order of the last common ancestor to all extant Mollusca. The ancient mitochondrial genome organization of C. apiculata is an important information that may help reconstructing the phylogeny of Mollusca and their relationship with other lophotrochozoans.
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Affiliation(s)
- Davide Guerra
- Université de Montréal, Département de Sciences Biologiques, 90 avenue Vincent-D'Indy, H2V 2S9 Montréal, Québec, Canada.
| | - Karim Bouvet
- Université de Montréal, Département de Sciences Biologiques, 90 avenue Vincent-D'Indy, H2V 2S9 Montréal, Québec, Canada.
| | - Sophie Breton
- Université de Montréal, Département de Sciences Biologiques, 90 avenue Vincent-D'Indy, H2V 2S9 Montréal, Québec, Canada.
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Detecting hybridization between sister species of Terebratulina (Brachiopoda, Cancellothyridoidea) in the North Atlantic: morphology versus molecules. Sci Rep 2017; 7:8845. [PMID: 28821797 PMCID: PMC5562858 DOI: 10.1038/s41598-017-09195-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/24/2017] [Indexed: 11/22/2022] Open
Abstract
Investigating samples of the cancellothyridid brachiopod Terebratulina collected during the IceAGE (Me85/3) expedition of RV METEOR at the continental shelf around Iceland with both morphometrical and molecular methods, we were for the first time able to detect a hybridization event between brachiopod sister species, which are thought to have separated 60 MYA. Terebratulina retusa and T. septentrionalis can clearly be distinguished on the basis of consistent species-specific molecular signatures in both mitochondrial and nuclear markers, whereas morphometrical analyses proved to be less reliable for species determination than previously thought. Two out of 28 specimens were identified as offspring of a one-way hybridization event between T. retusa eggs and T. septentrionalis sperm. Whereas the fossil record of Terebratulina in the North Atlantic region is too fragmentary to reconstruct the history of the hybridization event, the different life history traits of the two species and current oceanographic conditions around Iceland offer plausible explanations for the occurrence of crossbreeds in this common brachiopod genus.
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Phylogenetic investigations of Lingula anatina among some northwestern Pacific populations, based on mitochondrial DNA cytochrome c oxidase subunit I gene. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2017. [DOI: 10.1016/j.japb.2017.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Aguado MT, Richter S, Sontowski R, Golombek A, Struck TH, Bleidorn C. Syllidae mitochondrial gene order is unusually variable for Annelida. Gene 2016; 594:89-96. [DOI: 10.1016/j.gene.2016.08.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/21/2016] [Accepted: 08/29/2016] [Indexed: 01/16/2023]
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