1
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Complete mitochondrial genome of freshwater pearl mussel Lamellidens marginalis (Lamarck, 1819) and its phylogenetic relation within unionidae family. Mol Biol Rep 2022; 49:9593-9603. [DOI: 10.1007/s11033-022-07857-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/11/2022] [Indexed: 10/15/2022]
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2
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Saito T, Fujimoto K, Uchida S, Yamazaki D, Hirano T, Sano I, Ye B, Kagawa O, Shariar Shovon M, Tu Do V, Morii Y, Prozorova L, Chiba S. Uncovering overlooked diversity using molecular phylogenetic approach: a case of Japanese sphaeriid clams (Sphaeriidae: Bivalvia). Mol Phylogenet Evol 2022; 173:107508. [DOI: 10.1016/j.ympev.2022.107508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
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3
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Breton S, Stewart DT, Brémaud J, Havird JC, Smith CH, Hoeh WR. Did doubly uniparental inheritance (DUI) of mtDNA originate as a cytoplasmic male sterility (CMS) system? Bioessays 2022; 44:e2100283. [PMID: 35170770 PMCID: PMC9083018 DOI: 10.1002/bies.202100283] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 01/10/2023]
Abstract
Animal and plant species exhibit an astonishing diversity of sexual systems, including environmental and genetic determinants of sex, with the latter including genetic material in the mitochondrial genome. In several hermaphroditic plants for example, sex is determined by an interaction between mitochondrial cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Specifically, CMS involves aberrant mitochondrial genes that prevent pollen development and specific nuclear genes that restore it, leading to a mixture of female (male-sterile) and hermaphroditic individuals in the population (gynodioecy). Such a mitochondrial-nuclear sex determination system is thought to be rare outside plants. Here, we present one possible case of CMS in animals. We hypothesize that the only exception to the strict maternal mtDNA inheritance in animals, the doubly uniparental inheritance (DUI) system in bivalves, might have originated as a mitochondrial-nuclear sex-determination system. We document and explore similarities that exist between DUI and CMS, and we propose various ways to test our hypothesis.
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Affiliation(s)
- Sophie Breton
- Département des sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Donald T Stewart
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Julie Brémaud
- Département des sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Chase H Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Walter R Hoeh
- Department of Biological Sciences, Kent State University, Kent, Ohio, USA
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4
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Clewing C, Geertz T, Rassam H, Woldekiros TH, Albrecht C. Freshwater diversity at a biogeographic edge zone: the high-mountain pea-clams of Ethiopia. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2021.2005706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Catharina Clewing
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26 (IFZ), Giessen, 35390 Germany
| | - Thies Geertz
- International Foundation for Environment and Nature, Global Nature Fund (GNF), Radolfzell, Germany
| | - Hanane Rassam
- Muséum d’Histoire Naturelle de Marrakech, Laboratoire Hydrobiologie, Ecotoxicologie, Assainissement et Changements globaux, Université Cadi Ayyad, Marrakech, Morocco
| | | | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26 (IFZ), Giessen, 35390 Germany
- Department of Biology, Mbarara University of Science and Technology, Mbarara, Uganda
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5
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Maeda GP, Iannello M, McConie HJ, Ghiselli F, Havird JC. Relaxed selection on male mitochondrial genes in DUI bivalves eases the need for mitonuclear coevolution. J Evol Biol 2021; 34:1722-1736. [PMID: 34533872 DOI: 10.1111/jeb.13931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/21/2021] [Accepted: 09/05/2021] [Indexed: 12/31/2022]
Abstract
Mitonuclear coevolution is an important prerequisite for efficient energy production in eukaryotes. However, many bivalve taxa experience doubly uniparental inheritance (DUI) and have sex-specific mitochondrial (mt) genomes, providing a challenge for mitonuclear coevolution. We examined possible mechanisms to reconcile mitonuclear coevolution with DUI. No nuclear-encoded, sex-specific OXPHOS paralogs were found in the DUI clam Ruditapes philippinarum, refuting OXPHOS paralogy as a solution in this species. It is also unlikely that mt changes causing disruption of nuclear interactions are strongly selected against because sex-specific mt-residues or those under positive selection in M mt genes were not depleted for contacting nuclear-encoded residues. However, M genomes showed consistently higher dN /dS ratios compared to putatively ancestral F genomes in all mt OXPHOS genes and across all DUI species. Further analyses indicated that this was consistently due to relaxed, not positive selection on M vs. F mt OXPHOS genes. Similarly, selection was relaxed on the F genome of DUI species compared to species with strict maternal inheritance. Coupled with recent physiological and molecular evolution studies, we suggest that relaxed selection on M mt function limits the need to maintain mitonuclear interactions in M genomes compared to F genomes. We discuss our findings with regard to OXPHOS function and the origin of DUI.
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Affiliation(s)
- Gerald P Maeda
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Hunter J McConie
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
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6
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Porto-Hannes I, Burlakova LE, Zanatta DT, Lasker HR. Boundaries and hybridization in a secondary contact zone between freshwater mussel species (Family:Unionidae). Heredity (Edinb) 2021; 126:955-973. [PMID: 33883699 PMCID: PMC8178349 DOI: 10.1038/s41437-021-00424-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
Correct species identification and delineation are crucial for effective conservation and management. However, species delineation can be problematic in the presence of morphological ambiguities due to phenotypic plasticity, convergence, and/or interspecific hybridization. Here, we investigated the degree of hybridization between two closely related freshwater mussel species [Bivalvia: Unionidae; Lampsilis siliquoidea (Barnes) and L. radiata (Gmelin)] that present intermediate forms in areas of sympatry. Unionids have a distinct form of mitochondrial DNA (mtDNA) inheritance, termed doubly uniparental inheritance (DUI) where female mtDNA (F-type) is transmitted to all progeny but male mtDNA (M-type) is mostly inherited by the males resulting in mostly homoplasmic females and heteroplasmic males. An individual was identified as hybrid when F-type and M-type mtDNA of the two different species were found in the same individual. Twelve out of 116 sequenced males were identified as hybrids indicating that these species hybridize where their geographic range overlaps in the lower Great Lakes and St. Lawrence basins. Microsatellite analyses further support the occurrence of hybridization but at a larger spatial scale than indicated by the mitochondrial analyses. We also found that strong within-species population genetic structure affects the detection of purebred individuals overestimating the number of hybrids. Given the large geographic scale and proportion of hybrids found in this study, natural hybridization and introgression need to be considered when implementing local biodiversity inventories, identifying waterbodies as source of organisms for relocation and restoration projects and when setting appropriate conservation policies.
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Affiliation(s)
- Isabel Porto-Hannes
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA.
| | | | - David T Zanatta
- Institute for Great Lakes Research, Biology Department, Central Michigan University, Mount Pleasant, MI, USA
| | - Howard R Lasker
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA
- Department of Environment and Sustainability, University at Buffalo, Buffalo, NY, USA
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7
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Stewart DT, Stephenson CM, Stanton LM, Chase EE, Robicheau BM, Hoeh WR, Breton S. A proposed method for analyzing molecular signatures to detect hermaphroditism in freshwater mussels: a case study using the eastern floater (Pyganodon cataracta). CAN J ZOOL 2021. [DOI: 10.1139/cjz-2020-0166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Many freshwater mussels (order Unionida) have an unusual system of doubly uniparental inheritance (DUI) of mitochondrial (mt) DNA. In species with DUI, males possess a female-transmitted (F-type) mt genome and a male-transmitted (M-type) mt genome. These genomes contain non-canonical open reading frame (orf) genes, referred to as f-orf and m-orf, present in F and M mt genomes, respectively. These genes have been implicated in sexual development in Unionida. When gonochoric species become hermaphroditic, which has happened several times in Unionida, they lose their M-type mt genome and f-orf genes evolve dramatically. Resulting F-ORF proteins are highly divergent in terms of primary nucleotide sequence, inferred amino acids, and hydrophobic properties; these genes (and proteins) are referred to as hermaphroditic orfs or h-orfs (and H-ORFs). We investigated patterns of hydrophobicity divergence for H-ORF proteins in hermaphrodites versus F-ORF proteins in closely related gonochoric species against cytochrome c oxidase subunit 1 (cox1) divergences. This approach was used to assess whether cryptic hermaphrodites can be detected. Although we did not detect evidence for the recent transition of any populations of eastern floaters (Pyganodon cataracta (Say, 1817)) to hermaphroditism, our analyses demonstrate that molecular signatures in mtDNA can be used to detect hermaphroditism in freshwater mussels.
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Affiliation(s)
- Donald T. Stewart
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | | | | | - Emily E. Chase
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | | | - W. Randolph Hoeh
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Sophie Breton
- Département de sciences biologiques, Université de Montréal, QC H2V 0B3, Canada
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8
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Zieritz A, Froufe E, Bolotov I, Gonçalves DV, Aldridge DC, Bogan AE, Gan HM, Gomes-Dos-Santos A, Sousa R, Teixeira A, Varandas S, Zanatta D, Lopes-Lima M. Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian clade Contradentini+Rectidentini. We calculate substitution rates for the mitogenome, the 13 protein-coding genes, the two ribosomal units and three commonly used fragments (co1, nd1 and 16S) of both F- and M-mtDNA, based on a fossil-calibrated, mitogenomic phylogeny of the Unionidae. Phylogenetic analyses, including an M+F concatenated dataset, consistently recovers a monophyletic Gonideinae. Subfamily-level topology is congruent with that of a previous nuclear genomic study and with patterns in mitochondrial gene order, suggesting Unionidae F-type 2 as a synapomorphy of the Gonideinae. Our phylogeny indicates that the clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini split in the early Cretaceous (~125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (~79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type co1 and 16S for certain Unionidae and Margaritiferidae species (pairs).
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Affiliation(s)
- Alexandra Zieritz
- School of Geography, Sir Clive Granger Building, University of Nottingham, University Park, Nottingham, UK
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
| | - Ivan Bolotov
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk, Russian Federation
- Northern Arctic Federal University, Northern Dvina Emb. 17, Arkhangelsk, Russian Federation
- Saint-Petersburg State University, Universitetskaya Emb. 7/9, Saint Petersburg, Russian Federation
| | - Duarte V Gonçalves
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
| | - David C Aldridge
- Aquatic Ecology Group, The David Attenborough Building, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Arthur E Bogan
- Research Laboratory, North Carolina State Museum of Natural Sciences, Raleigh, NC, USA
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong,, VIC, Australia
| | - André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, Porto, Portugal
| | - Ronaldo Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campos de Gualtar, Braga, Portugal
| | - Amilcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
| | - Simone Varandas
- CITAB-UTAD – Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Apartado 1013, Vila Real, Portugal
| | - David Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Biosciences, Mount Pleasant, MI, USA
| | - Manuel Lopes-Lima
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Portugal
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9
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Soroka M. Doubly uniparental inheritance of mitochondrial DNA in freshwater mussels: History and status of the European species. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Burzyński A, Soroka M. Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae). PeerJ 2018; 6:e5573. [PMID: 30221094 PMCID: PMC6138038 DOI: 10.7717/peerj.5573] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/13/2018] [Indexed: 12/22/2022] Open
Abstract
Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent.
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Affiliation(s)
- Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Marianna Soroka
- University of Szczecin, Faculty of Biology, Department of Genetics, Szczecin, Poland
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11
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Chase EE, Robicheau BM, Veinot S, Breton S, Stewart DT. The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida. BMC Genomics 2018; 19:221. [PMID: 29587633 PMCID: PMC5870820 DOI: 10.1186/s12864-018-4583-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/07/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Doubly uniparental inheritance (DUI) of mitochondrial DNA in bivalves is a fascinating exception to strictly maternal inheritance as practiced by all other animals. Recent work on DUI suggests that there may be unique regions of the mitochondrial genomes that play a role in sex determination and/or sexual development in freshwater mussels (order Unionoida). In this study, one complete mitochondrial genome of the hermaphroditic swan mussel, Anodonta cygnea, is sequenced and compared to the complete mitochondrial genome of the gonochoric duck mussel, Anodonta anatina. An in silico assessment of novel proteins found within freshwater bivalve species (known as F-, H-, and M-open reading frames or ORFs) is conducted, with special attention to putative transmembrane domains (TMs), signal peptides (SPs), signal cleavage sites (SCS), subcellular localization, and potential control regions. Characteristics of TMs are also examined across freshwater mussel lineages. RESULTS In silico analyses suggests the presence of SPs and SCSs and provides some insight into possible function(s) of these novel ORFs. The assessed confidence in these structures and functions was highly variable, possibly due to the novelty of these proteins. The number and topology of putative TMs appear to be maintained among both F- and H-ORFs, however, this is not the case for M-ORFs. There does not appear to be a typical control region in H-type mitochondrial DNA, especially given the loss of tandem repeats in unassigned regions when compared to F-type mtDNA. CONCLUSION In silico analyses provides a useful tool to discover patterns in DUI and to navigate further in situ analyses related to DUI in freshwater mussels. In situ analysis will be necessary to further explore the intracellular localizations and possible role of these open reading frames in the process of sex determination in freshwater mussel.
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Affiliation(s)
- E. E. Chase
- Department of Biology, Acadia University, Wolfville, NS Canada
| | - B. M. Robicheau
- Department of Biology, Dalhousie University, Halifax, NS Canada
| | - S. Veinot
- Department of Biology, Dalhousie University, Halifax, NS Canada
| | - S. Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - D. T. Stewart
- Department of Biology, Acadia University, Wolfville, NS Canada
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12
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Lim JY, Tay TS, Lim CS, Lee SSC, Teo SLM, Tan KS. Mytella strigata (Bivalvia: Mytilidae): an alien mussel recently introduced to Singapore and spreading rapidly. MOLLUSCAN RESEARCH 2018. [DOI: 10.1080/13235818.2018.1423858] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- J. Y. Lim
- St John’s Island National Marine Laboratory, Tropical Marine Science Institute, National University of Singapore, Singapore, 119227
| | - T. S. Tay
- St John’s Island National Marine Laboratory, Tropical Marine Science Institute, National University of Singapore, Singapore, 119227
| | - C. S. Lim
- St John’s Island National Marine Laboratory, Tropical Marine Science Institute, National University of Singapore, Singapore, 119227
| | - S. S. C. Lee
- St John’s Island National Marine Laboratory, Tropical Marine Science Institute, National University of Singapore, Singapore, 119227
| | - S. L.-M. Teo
- St John’s Island National Marine Laboratory, Tropical Marine Science Institute, National University of Singapore, Singapore, 119227
| | - K. S. Tan
- St John’s Island National Marine Laboratory, Tropical Marine Science Institute, National University of Singapore, Singapore, 119227
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13
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Soroka M, Burzyński A. Hermaphroditic freshwater mussel Anodonta cygnea does not have supranumerary open reading frames in the mitogenome. Mitochondrial DNA B Resour 2017; 2:862-864. [PMID: 33474013 PMCID: PMC7800200 DOI: 10.1080/23802359.2017.1407705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 11/17/2017] [Indexed: 11/10/2022] Open
Abstract
The complete mitogenome of Anodonta cygnea is 15,613 bp long. This compact, circular molecule contains the set of 37 genes, typical for invertebrate mitogenomes, in the same order and orientation as in maternally inherited genomes of other bivalves from the same subfamily. There are only two unassigned regions longer than 200 bp (266 bp and 274 bp) and no indication of any supranumerary open reading frames.
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Affiliation(s)
- Marianna Soroka
- Department of Genetics, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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14
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Mioduchowska M, Kaczmarczyk A, Zając K, Zając T, Sell J. Gender-Associated Mitochondrial DNA Heteroplasmy in Somatic Tissues of the Endangered Freshwater Mussel Unio crassus (Bivalvia: Unionidae): Implications for Sex Identification and Phylogeographical Studies. ACTA ACUST UNITED AC 2017; 325:610-625. [PMID: 28102008 DOI: 10.1002/jez.2055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/11/2016] [Accepted: 10/24/2016] [Indexed: 11/11/2022]
Abstract
Some bivalve species possess two independent mitochondrial DNA lineages: maternally (F-type) and paternally (M-type) inherited. This phenomenon is called doubly uniparental inheritance. It is generally agreed that F-type mtDNA is typically present in female somatic and gonadal tissues as well as in male somatic tissues, whereas the M-type mtDNA occurs only in male germ line and gonadal tissue. In the present study, the mtDNA heteroplasmy (for both F and M genomes) in male somatic tissues of Unio crassus (Philipsson, 1788), species threatened with extinction, has been confirmed. Taking advantage from the presence of Mcox1 marker only in male somatic tissues, we developed a new method of sex identification in this endangered species, using nondestructive tissue sampling. Probability of correct sex identification was estimated at 97.5%. The present study is the first report on gender-associated mitochondrial DNA heteroplasmy in male somatic tissues of thick-shelled river mussel and first approach to U. crassus sex identification at molecular level. Our study also confirmed the utility of paternally inherited Mcox1 gene fragment as a complementary molecular tool for resolving phylogeographical relationships among populations of thick-shelled river mussel.
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Affiliation(s)
| | | | - Katarzyna Zając
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Krakow, Poland
| | - Tadeusz Zając
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Krakow, Poland
| | - Jerzy Sell
- Department of Genetics, University of Gdansk, 80-308 Gdansk, Poland
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15
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Vikhrev IV, Bolotov IN, Altun A, Gofarov MY, Dvoryankin GA, Kondakov AV, Ozcan T, Ozcan G. The revenant: rediscovery of Margaritifera homsensis from Orontes drainage with remarks on its taxonomic status and conservation (Bivalvia: Margaritiferidae). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1343876] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Ilya V. Vikhrev
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Ivan N. Bolotov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Ayhan Altun
- Faculty of Marine Sciences and Technology, Iskenderun Technical University, Iskenderun 31200, Hatay, Turkey
| | - Mikhail Y. Gofarov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Gennady A. Dvoryankin
- SevPINRO – Northern Branch of the Polar Scientific-Research Institute of Fish Husbandry and Oceanography, Uritskogo 17, Arkhangelsk 163000, Russian Federation
| | - Alexander V. Kondakov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Tahir Ozcan
- Faculty of Marine Sciences and Technology, Iskenderun Technical University, Iskenderun 31200, Hatay, Turkey
| | - Gulnaz Ozcan
- Faculty of Marine Sciences and Technology, Iskenderun Technical University, Iskenderun 31200, Hatay, Turkey
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16
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Next generation sequencing of gonadal transcriptome suggests standard maternal inheritance of mitochondrial DNA in Eurhomalea rufa (Veneridae). Mar Genomics 2017. [DOI: 10.1016/j.margen.2016.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Robicheau BM, Powell AE, Del Bel L, Breton S, Stewart DT. Evidence for extreme sequence divergence between the male- and female-transmitted mitochondrial genomes in the bivalve mollusc,Modiolus modiolus(Mytilidae). J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Amy E. Powell
- Faculty of Medicine; Memorial University; Saint John's NFL Canada
| | | | - Sophie Breton
- Departement de Science Biologiques; Université de Montréal; Montreal QC Canada
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18
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Gusman A, Lecomte S, Stewart DT, Passamonti M, Breton S. Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA. PeerJ 2016; 4:e2760. [PMID: 27994972 PMCID: PMC5157197 DOI: 10.7717/peerj.2760] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 11/05/2016] [Indexed: 11/20/2022] Open
Abstract
There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA) in the animal kingdom: a system named doubly uniparental inheritance (DUI), which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI) in two bivalve species, i.e., the nuculanoid Yoldia hyperborea(Gould, 1841)and the veneroid Scrobicularia plana(Da Costa,1778), increasing the number of families in which DUI has been found by two. An update on the taxonomic distribution of DUI in the Bivalvia is also presented.
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Affiliation(s)
- Arthur Gusman
- Department of Biological Sciences, Université de Montréal , Montréal , Québec , Canada
| | - Sophia Lecomte
- Department of Biological Sciences, Université de Strasbourg , Strasbourg , France
| | - Donald T Stewart
- Department of Biology, Acadia University , Wolfville , Nova Scotia , Canada
| | - Marco Passamonti
- Department of Biological Geological and Environmental Sciences, University of Bologna , Bologna , Italy
| | - Sophie Breton
- Department of Biological Sciences, Université de Montréal , Montréal , Québec , Canada
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19
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The complete maternal and paternal mitochondrial genomes of Unio crassus: Mitochondrial molecular clock and the overconfidence of molecular dating. Mol Phylogenet Evol 2016; 107:605-608. [PMID: 27956259 DOI: 10.1016/j.ympev.2016.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 11/21/2022]
Abstract
The availability of a rapidly growing number of complete mitochondrial genome sequences provokes high confidence dating approaches. However, even if the congruence between mitochondrial and nuclear markers is reasonable, the resulting topologies are frequently questionable. The unique opportunity to study the evolutionary history of two independent mitochondrial genomes in one phylogenetic context exists in the freshwater mussels family Unionidae. The two lineages function under doubly uniparental inheritance since well before the emergence of the family. Despite the relatively high number of available complete sequences of maternally inherited genomes, comparative analyses are limited by the small number of sequences of counterpart paternally inherited genomes. We have sequenced for the first time the representative set of five sequences (two maternal and three paternal) from the species Unio crassus. Comparative analysis of the phylogenies reconstructed using relevant mitogenomic data available in GenBank (13 species in total) reveal that single - genome inferences are congruent only if the relaxed clock is assumed.
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20
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Lopes-Lima M, Froufe E, Do VT, Ghamizi M, Mock KE, Kebapçı Ü, Klishko O, Kovitvadhi S, Kovitvadhi U, Paulo OS, Pfeiffer JM, Raley M, Riccardi N, Şereflişan H, Sousa R, Teixeira A, Varandas S, Wu X, Zanatta DT, Zieritz A, Bogan AE. Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes. Mol Phylogenet Evol 2016; 106:174-191. [PMID: 27621130 DOI: 10.1016/j.ympev.2016.08.021] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/08/2016] [Accepted: 08/30/2016] [Indexed: 11/15/2022]
Abstract
Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032bp (COI+28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.
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Affiliation(s)
- Manuel Lopes-Lima
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Van Tu Do
- Department of Aquatic Ecology, Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Viet Nam
| | - Mohamed Ghamizi
- Muséum d'Histoire Naturelle de Marrakech, Université Cadi Ayyad, Faculté des Sciences, Semlalia, B.P. 2390 Marrakech, Morocco
| | - Karen E Mock
- Ecology Center and Department of Wildland Resources, Utah State University, Logan, UT 84322, USA
| | - Ümit Kebapçı
- Department of Biology, Faculty of Arts and Sciences, Mehmet Akif Ersoy University, Burdur, Turkey
| | - Olga Klishko
- Institute of Natural Resources, Ecology and Criology, Russian Academy of Sciences Siberian Branch, Chita 672014, Russia
| | - Satit Kovitvadhi
- Department of Agriculture, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok 10600, Thailand
| | - Uthaiwan Kovitvadhi
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - John M Pfeiffer
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | | | - Hülya Şereflişan
- Faculty of Marine Sciences and Technology, İskenderun Technical University, 31200 Iskenderun, Hatay, Turkey
| | - Ronaldo Sousa
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Amílcar Teixeira
- CIMO/ESA/IPB - Mountain Research Centre, School of Agriculture, Polytechnic Institute of Bragança, Campus de Santa Apolónia, Apartado 1172, 5301-854 Bragança, Portugal
| | - Simone Varandas
- CITAB/UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, 5000-801 Vila Real, Portugal
| | - Xiaoping Wu
- School of Life Sciences, Center for Watershed Ecology, Institute of Life Science, Nanchang University, Nanchang 330031, People's Republic of China
| | - David T Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Biosciences Bldg. 2408, Mount Pleasant, MI 48859, USA
| | - Alexandra Zieritz
- School of Geography, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Malaysia
| | - Arthur E Bogan
- Research Laboratory, North Carolina State Museum of Natural Sciences, MSC 1626, Raleigh, NC 27699-1626, USA
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21
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Amaro R, Bouza C, Pardo BG, Castro J, San Miguel E, Villalba A, Lois S, Outeiro A, Ondina P. Identification of novel gender-associated mitochondrial haplotypes in Margaritifera margaritifera(Linnaeus, 1758). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Rafaela Amaro
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Carmen Bouza
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Belén G. Pardo
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Jaime Castro
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Eduardo San Miguel
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas de Corón (CIMA); Consellería do Medio Rural e do Mar da Xunta de Galicia; Aptdo. 13 36620 Vilanova de Arousa Spain
| | - Sabela Lois
- Department of Zoology; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Adolfo Outeiro
- Department of Zoology; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Paz Ondina
- Department of Zoology; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
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22
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Bettinazzi S, Plazzi F, Passamonti M. The Complete Female- and Male-Transmitted Mitochondrial Genome of Meretrix lamarckii. PLoS One 2016; 11:e0153631. [PMID: 27083010 PMCID: PMC4833323 DOI: 10.1371/journal.pone.0153631] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/02/2016] [Indexed: 11/17/2022] Open
Abstract
Bivalve mitochondrial genomes show many uncommon features, like additional genes, high rates of gene rearrangement, high A-T content. Moreover, Doubly Uniparental Inheritance (DUI) is a distinctive inheritance mechanism allowing some bivalves to maintain and transmit two separate sex-linked mitochondrial genomes. Many bivalve mitochondrial features, such as gene extensions or additional ORFs, have been proposed to be related to DUI but, up to now, this topic is far from being understood. Several species are known to show this unusual organelle inheritance but, being widespread only among Unionidae and Mytilidae, DUI distribution is unclear. We sequenced and characterized the complete female- (F) and male-transmitted (M) mitochondrial genomes of Meretrix lamarckii, which, in fact, is the second species of the family Veneridae where DUI has been demonstrated so far. The two mitochondrial genomes are comparable in length and show roughly the same gene content and order, except for three additional tRNAs found in the M one. The two sex-linked genomes show an average nucleotide divergence of 16%. A 100-aminoacid insertion in M. lamarckii M-cox2 gene was found; moreover, additional ORFs have been found in both F and M Long Unassigned Regions of M. lamarckii. Even if no direct involvement in DUI process has been demonstrated so far, the finding of cox2 insertions and supernumerary ORFs in M. lamarckii both strengthens this hypothesis and widens the taxonomical distribution of such unusual features. Finally, the analysis of inter-sex genetic variability shows that DUI species form two separate clusters, namely Unionidae and Mytilidae+Veneridae; this dichotomy is probably due to different DUI regimes acting on separate taxa.
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Affiliation(s)
- Stefano Bettinazzi
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, BO, Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, BO, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, BO, Italy
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23
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Santos-Neto GDC, Beasley CR, Schneider H, Pimpão DM, Hoeh WR, Simone LRLD, Tagliaro CH. Genetic relationships among freshwater mussel species from fifteen Amazonian rivers and inferences on the evolution of the Hyriidae (Mollusca: Bivalvia: Unionida). Mol Phylogenet Evol 2016; 100:148-159. [PMID: 27071805 DOI: 10.1016/j.ympev.2016.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 03/19/2016] [Accepted: 04/09/2016] [Indexed: 10/22/2022]
Abstract
The current phylogenetic framework for the South American Hyriidae is solely based on morphological data. However, freshwater bivalve morphology is highly variable due to both genetic and environmental factors. The present study used both mitochondrial (COI and 16S) and nuclear (18S-ITS1) sequences in molecular phylogenetic analyses of nine Neotropical species of Hyriidae, collected from 15 South American rivers, and sequences of hyriids from Australia and New Zealand obtained from GenBank. The present molecular findings support traditional taxonomic proposals, based on morphology, for the South American subfamily Hyriinae, currently divided in three tribes: Hyriini, Castaliini and Rhipidodontini. Phylogenetic trees based on COI nucleotide sequences revealed at least four geographical groups of Castalia ambigua: northeast Amazon (Piriá, Tocantins and Caeté rivers), central Amazon, including C. quadrata (Amazon and Aripuanã rivers), north (Trombetas river), and C. ambigua from Peru. Genetic distances suggest that some specimens may be cryptic species. Among the Hyriini, a total evidence data set generated phylogenetic trees indicating that Paxyodon syrmatophorus and Prisodon obliquus are more closely related, followed by Triplodon corrugatus. The molecular clock, based on COI, agreed with the fossil record of Neotropical hyriids. The ancestor of both Australasian and Neotropical Hyriidae is estimated to have lived around 225million years ago.
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Affiliation(s)
- Guilherme da Cruz Santos-Neto
- Laboratório de Conservação e Biologia Evolutiva, Instituto de Estudos Costeiros, Campus de Bragança, Universidade Federal do Pará, Alameda Leandro Ribeiro, s/n, Bairro Aldeia, Bragança, Pará CEP 68600-000, Brazil; Instituto Federal de Educação, Ciência e Tecnologia do Pará, Campus Abaetetuba, Rua Rio de Janeiro, 2233, Bairro Francilândia, Abaetetuba, Pará CEP 68440-000, Brazil.
| | - Colin Robert Beasley
- Laboratório de Moluscos, Instituto de Estudos Costeiros, Campus de Bragança, Universidade Federal do Pará, Alameda Leandro Ribeiro, s/n, Bairro Aldeia, Bragança, Pará CEP 68600-000, Brazil
| | - Horacio Schneider
- Laboratório de Biologia Molecular, Instituto de Estudos Costeiros, Campus de Bragança, Universidade Federal do Pará, Alameda Leandro Ribeiro, s/n, Bairro Aldeia, Bragança, Pará CEP 68600-000, Brazil
| | - Daniel Mansur Pimpão
- Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, Superintendência Regional no Goiás, Rua 229 n°95, Leste Universitário, Goiania, Goiás CEP 74605-090, Brazil
| | - Walter Randolph Hoeh
- Department of Biological Sciences, Kent State University, Cunningham Hall, Summit Street, Kent, OH 44242, USA
| | | | - Claudia Helena Tagliaro
- Laboratório de Conservação e Biologia Evolutiva, Instituto de Estudos Costeiros, Campus de Bragança, Universidade Federal do Pará, Alameda Leandro Ribeiro, s/n, Bairro Aldeia, Bragança, Pará CEP 68600-000, Brazil.
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24
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Bößneck U, Clewing C, Albrecht C. Exploring high-mountain limnic faunas: discovery of a novel endemic bivalve species (Sphaeriidae : Pisidium) in the Nepal Himalayas. INVERTEBR SYST 2016. [DOI: 10.1071/is15043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
High-mountain regions are known to harbour considerable biodiversity, although it is not all well known. The terrestrial fauna of the world’s largest mountain range, the Himalayas, has been moderately well studied, but this is not the case with the limnic fauna, and especially molluscs. During intensive malacozoological field surveys conducted over the past 20 years, the bivalve family Sphaeriidae has been studied in Nepal along an elevational gradient from 100 to 4010 m above sea level (a.s.l.). Here we describe a new species of Sphaeriidae, Pisidium alexeii, sp. nov., based on comprehensive molecular phylogenetics, anatomy and shell morphology. The species can be clearly distinguished from all other sphaeriid species occurring in Nepal. A molecular phylogeny based on mitochondrial and nuclear data inferred the oriental biogeographical affinity of the new species. The species is ecologically restricted and only occurs at a few sites between 1010 and 1700 m a.s.l. A review and updated checklist of the sphaeriid fauna of Nepal is provided and biodiversity and biogeographical patterns are discussed.
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25
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Vargas J, Pérez M, Toro J, Astorga MP. Presence of two mitochondrial genomes in the mytilid Perumytilus purpuratus: Phylogenetic evidence for doubly uniparental inheritance. Genet Mol Biol 2015; 38:173-81. [PMID: 26273220 PMCID: PMC4530645 DOI: 10.1590/s1415-47573822201420140262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 01/22/2015] [Indexed: 11/24/2022] Open
Abstract
This study presents evidence, using sequences of ribosomal 16S and COI mtDNA, for the presence of two mitochondrial genomes in Perumytilus purpuratus. This may be considered evidence of doubly uniparental mtDNA inheritance. The presence of the two types of mitochondrial genomes differentiates females from males. The F genome was found in the somatic and gonadal tissues of females and in the somatic tissues of males; the M genome was found in the gonads and mantle of males only. For the mitochondrial 16S region, ten haplotypes were found for the F genome (nucleotide diversity 0.004), and 7 haplotypes for the M genome (nucleotide diversity 0.001), with a distance Dxy of 0.125 and divergence Kxy of 60.33%. For the COI gene 17 haplotypes were found for the F genome (nucleotide diversity 0.009), and 10 haplotypes for the M genome (nucleotide diversity 0.010), with a genetic distance Dxy of 0.184 and divergence Kxy of 99.97%. Our results report the presence of two well-differentiated, sex-specific types of mitochondrial genome (one present in the male gonad, the other in the female gonad), implying the presence of DUI in P. purpuratus. These results indicate that care must be taken in phylogenetic comparisons using mtDNA sequences of P. purpuratus without considering the sex of the individuals.
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Affiliation(s)
- Jaime Vargas
- Instituto de Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile
| | - Montse Pérez
- > Instituto Español de Oceanografía. Centro Oceanográfico de Vigo, Vigo, Spain
| | - Jorge Toro
- Instituto de Ciencias Marinas y Limnológicas. Universidad Austral de Chile, Valdivia, Chile
| | - Marcela P Astorga
- Instituto de Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile
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26
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Machordom A, Araujo R, Toledo C, Zouros E, Ladoukakis ED. Female-dependent transmission of paternal mtDNA is a shared feature of bivalve species with doubly uniparental inheritance (DUI) of mitochondrial DNA. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12096] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Annie Machordom
- Biodiversity and Evolutionary Biology Department; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - Rafael Araujo
- Biodiversity and Evolutionary Biology Department; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - Carlos Toledo
- Biodiversity and Evolutionary Biology Department; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
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27
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Plazzi F. The detection of sex-linked heteroplasmy in Pseudocardium sachalinense
(Bivalvia: Mactridae) and its implications for the distribution of doubly uniparental inheritance of mitochondrial DNA. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Federico Plazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali; University of Bologna; Bologna BO Italy
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28
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Soroka M, Burzyński A. Complete male mitochondrial genome of Anodonta anatina (Mollusca: Unionidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1679-80. [PMID: 25317641 DOI: 10.3109/19401736.2014.958725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Anodonta anatina is a freshwater mussel of the family Unionidae. These mussels have a unique mitochondria inheritance system named doubly uniparental inheritance (DUI). Under DUI males have two, potentially very divergent mitochondrial genomes: F-type inherited from mother and M-type inherited from father. F-type is present in soma whereas M-type is present in gonadal tissues and sperm. Here we report two M-type sequences of complete mitochondrial genomes from Anodonta anatina. They are 16,906 bp long and their sequences are similar (0.1% divergence). The genome organization is identical to the other Unionidean M-type genomes published to date. There are 38 genes, including the recently described M-type specific M ORF. The presence of tRNA-like repeat in one of the noncoding regions, suggests that the control region is located in this area. Nucleotide composition is quite extreme, with AT content (66.2%) higher than in any other of the six published Unionidean M genomes.
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Affiliation(s)
- Marianna Soroka
- a Department of Genetics , University of Szczecin , Szczecin , Poland
| | - Artur Burzyński
- b Institute of Oceanology, Polish Academy of Sciences , Sopot , Poland , and.,c Institute of Biology and Environmental Protection, Pommeranian University in Słupsk , Poland
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29
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Plazzi F, Cassano A, Passamonti M. The quest for Doubly Uniparental Inheritance in heterodont bivalves and its detection inMeretrix lamarckii(Veneridae: Meretricinae). J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12078] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Federico Plazzi
- Dipartimento di Scienze Biologiche; Geologiche e Ambientali; Bologna Italy
| | - Antonello Cassano
- Dipartimento di Scienze Biologiche; Geologiche e Ambientali; Bologna Italy
| | - Marco Passamonti
- Dipartimento di Scienze Biologiche; Geologiche e Ambientali; Bologna Italy
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30
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Marshall BA, Fenwick MC, Ritchie PA. New Zealand Recent Hyriidae (Mollusca: Bivalvia: Unionida). MOLLUSCAN RESEARCH 2014. [DOI: 10.1080/13235818.2014.889591] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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31
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Sańko TJ, Burzyński A. Co-expressed mitochondrial genomes: recently masculinized, recombinant mitochondrial genome is co-expressed with the female-transmitted mtDNA genome in a male Mytilus trossulus mussel from the Baltic Sea. BMC Genet 2014; 15:28. [PMID: 24575766 PMCID: PMC3941564 DOI: 10.1186/1471-2156-15-28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 02/13/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Few exceptions have been described from strict maternal inheritance of mitochondrial DNA in animals, including sea mussels (Mytilidae), clams (Donacidae, Veneridae and Solenidae) and freshwater mussels (Unionoidae) order. In these bivalves mitochondria and their DNA are transferred through two separate routes. The females inherit only the maternal mitochondrial DNA whereas the males inherit maternal as well as paternal mitochondrial DNA, which is usually present only in gonads and sperm. The mechanism controlling this phenomenon is unclear but leads to the existence of two separate mitochondrial DNA lineages in a single species. The lineages are usually well differentiated: up to 20-50% divergence in nucleotide sequence. Occasionally, a maternal mitochondrial DNA can invade the paternal transmission route, eventually replacing the diverged M-type and lowering the divergence. Such role reversal (masculinization) event has happened recently in the Mytilus population of the Baltic Sea which consists of M. edulis × M. trossulus hybrids, but the functional status of the resulting mitochondrial genome was unknown. RESULTS In this paper we sequenced transcripts from one specimen that was identified as male carrying both the female mitochondrial genome and a recently masculinized mitochondrial genome. Additionally, the analysis of the control region has showed that the recently masculinized, recombinant genome, not only has an M-type control region and all coding regions derived from the F-type, but also is transcriptionally active along side the maternally inherited F-type genome. In the comparative analysis, the two genomes exhibit different substitution patterns, typical for the M vs. F genome comparisons. The genetic distances and ratios of non-synonymous substitutions also suggest that one of the genomes is transitioning from the maternal to the paternal inheritance mode, consistent with its recent masculinization. CONCLUSION We have shown, for the first time, that the recently masculinized mitochondrial genome is active and that it accumulates excess of non-synonymous substitutions across its coding sequence. This suggests, that, under certain cytonuclear incompatibility conditions, masculinization may serve to restore the endangered functionality of the paternally inherited genome. This is also another example of a mitochondrial genome in which the recombination in the control region predated its transition from paternal to maternal transmission route.
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Affiliation(s)
- Tomasz J Sańko
- Genetics and Marine Biotechnology Department, Institute of Oceanology of Polish Academy of Sciences, Powstańców Warszawy 55, Sopot 81-712, Poland.
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Clewing C, Bössneck U, Oheimb PVV, Albrecht C. Molecular Phylogeny and Biogeography of a High Mountain Bivalve Fauna: The Sphaeriidae of the Tibetan Plateau. MALACOLOGIA 2013. [DOI: 10.4002/040.056.0213] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Krebs RA, Borden WC, Evans NM, Doerder FP. Differences in population structure estimated within maternally- and paternally-inherited forms of mitochondria inLampsilis siliquoidea(Bivalvia: Unionidae). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert A. Krebs
- Department of Biological, Geological, and Environmental Sciences; Cleveland State University; Cleveland; OH; 44115-2406; USA
| | - W. Calvin Borden
- Department of Biology; Loyola University Chicago; Chicago; IL; 60660; USA
| | - Na'tasha M. Evans
- Department of Biological, Geological, and Environmental Sciences; Cleveland State University; Cleveland; OH; 44115-2406; USA
| | - F. Paul Doerder
- Department of Biological, Geological, and Environmental Sciences; Cleveland State University; Cleveland; OH; 44115-2406; USA
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Shepardson SP, Heard WH, Breton S, Hoeh WR. Light and Transmission Electron Microscopy of Two Spermatogenic Pathways and Unimorphic Spermatozoa inVenustaconcha ellipsiformis(Conrad, 1836) (Bivalvia: Unionoida). MALACOLOGIA 2012. [DOI: 10.4002/040.055.0207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Stewart DT, Jha M, Breton S, Hoeh WR, Blier PU. No effect of sperm interactions or egg homogenate on sperm velocity in the blue mussel, Mytilus edulis (Bivalvia: Mytilidae). CAN J ZOOL 2012. [DOI: 10.1139/z2012-099] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigated the possible effects of sperm interactions and homogenized eggs on sperm velocity in blue mussels ( Mytilus edulis L., 1758) using computer-assisted sperm analysis. To test whether sperm competition results in an increase in sperm velocity, using seven pairs of males, we compared the mean curvilinear and average path velocities of sperm from two males measured separately with the corresponding values from a mixture of sperm from the same two males. To test whether the presence of eggs results in an increase in sperm velocity, we compared curvilinear and average path velocities from 11 individual males with the corresponding measures from the same 11 sperm samples mixed with aliquots of homogenized eggs. Neither experimental treatment resulted in an increase in sperm velocity. We interpret these results as consistent with the hypothesis that mussel sperm have been selected to immediately begin swimming at an optimal initial velocity that is adaptive for the particular environment in which they are located. Critical factors affecting the evolution of sperm velocity for broadcast spawning, external fertilizers such as M. edulis likely include population density and intraspecific spawning synchronicity. As has been suggested by others, the importance of sperm limitation (i.e., having much less than 100% of eggs being fertilized in the wild) may be as important an evolutionary driving force in broadcast spawning invertebrates as sperm competition is in internally or directly fertilized species.
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Affiliation(s)
- Donald T. Stewart
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - Mamta Jha
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - Sophie Breton
- Robert-Cedergren Center for Bioinformatics and Genomics, Department of Biochemistry, Pavillon Roger Gaudry (P. principal) H-307-13, Université de Montréal, 2900 Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - W. Randolph Hoeh
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Pierre U. Blier
- Département de biologie, Université du Québec à Rimouski, 300, allée des Ursulines, Rimouski, QC G5L 3A1, Canada
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Stanton L, Hoeh W, McAlpine D, Hebda A, Stewart D. mtDNA and AFLP markers demonstrate limited genetic differentiation within the Pyganodon cataracta–Pyganodon fragilis freshwater mussel complex in Atlantic Canada. CAN J ZOOL 2012. [DOI: 10.1139/z2012-100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two nominal species of freshwater mussels, Pyganodon cataracta (Say, 1817) (eastern floater) and Pyganodon fragilis (Lamarck, 1819) (Newfoundland floater), occur in Atlantic Canada, but their taxonomic status has been controversial. We analyzed the female-transmitted mitochondrial cytochrome c oxidase subunit I (i.e., FCOI) and nuclear internal transcribed spacer region (ITS-1) gene sequences, as well as multilocus amplified fragment length polymorphism (AFLP) markers, to evaluate genetic variation in Pyganodon specimens from Atlantic Canada. We found that Pyganodon samples from this region displayed no or extremely low (i.e., <0.5%) genetic divergence for ITS-1 and FCOI sequence data, respectively. Inferences from nested clade analysis of FCOI haplotypes suggest restricted gene flow with isolation by distance and contiguous range expansion. Analysis of molecular variance inferred from presence or absence of nuclear-encoded AFLP bands showed moderate geographic structuring among provinces but no correspondence between mtDNA haplotypes and AFLP profiles. Similarly, there was no correspondence between presence of a single or a double loop on the umbo and FCOI haplotype. These mtDNA and AFLP markers demonstrate limited genetic differentiation within the Pyganodon cataracta–Pyganodon fragilis freshwater mussel complex in Atlantic Canada and question the species-level distinctness of these putative taxa.
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Affiliation(s)
- L.M. Stanton
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - W.R. Hoeh
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - D.F. McAlpine
- Department of Natural Science, New Brunswick Museum, Saint John, NB E2K 1E5, Canada
| | - A. Hebda
- Nova Scotia Museum of Natural History (Zoology), Halifax, NS B3H 3A6, Canada
| | - D.T. Stewart
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
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Biparental Inheritance Through Uniparental Transmission: The Doubly Uniparental Inheritance (DUI) of Mitochondrial DNA. Evol Biol 2012. [DOI: 10.1007/s11692-012-9195-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Pyganodon (Bivalvia: Unionoida: Unionidae) phylogenetics: A male- and female-transmitted mitochondrial DNA perspective. Mol Phylogenet Evol 2012; 63:430-44. [DOI: 10.1016/j.ympev.2012.01.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 01/17/2012] [Accepted: 01/20/2012] [Indexed: 11/21/2022]
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Obata M, Sano N, Komaru A. Different transcriptional ratios of male and female transmitted mitochondrial DNA and tissue-specific expression patterns in the blue mussel, Mytilus galloprovincialis. Dev Growth Differ 2011; 53:878-86. [DOI: 10.1111/j.1440-169x.2011.01294.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Breton S, Ghiselli F, Passamonti M, Milani L, Stewart DT, Hoeh WR. Evidence for a fourteenth mtDNA-encoded protein in the female-transmitted mtDNA of marine Mussels (Bivalvia: Mytilidae). PLoS One 2011; 6:e19365. [PMID: 21556327 PMCID: PMC3083442 DOI: 10.1371/journal.pone.0019365] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 04/02/2011] [Indexed: 11/30/2022] Open
Abstract
Background A novel feature for animal mitochondrial genomes has been recently established: i.e., the presence of additional, lineage-specific, mtDNA-encoded proteins with functional significance. This feature has been observed in freshwater mussels with doubly uniparental inheritance of mtDNA (DUI). The latter unique system of mtDNA transmission, which also exists in some marine mussels and marine clams, is characterized by one mt genome inherited from the female parent (F mtDNA) and one mt genome inherited from the male parent (M mtDNA). In freshwater mussels, the novel mtDNA-encoded proteins have been shown to be mt genome-specific (i.e., one novel protein for F genomes and one novel protein for M genomes). It has been hypothesized that these novel, F- and M-specific, mtDNA-encoded proteins (and/or other F- and/or M-specific mtDNA sequences) could be responsible for the different modes of mtDNA transmission in bivalves but this remains to be demonstrated. Methodology/Principal Findings We investigated all complete (or nearly complete) female- and male-transmitted marine mussel mtDNAs previously sequenced for the presence of ORFs that could have functional importance in these bivalves. Our results confirm the presence of a novel F genome-specific mt ORF, of significant length (>100aa) and located in the control region, that most likely has functional significance in marine mussels. The identification of this ORF in five Mytilus species suggests that it has been maintained in the mytilid lineage (subfamily Mytilinae) for ∼13 million years. Furthermore, this ORF likely has a homologue in the F mt genome of Musculista senhousia, a DUI-containing mytilid species in the subfamily Crenellinae. We present evidence supporting the functionality of this F-specific ORF at the transcriptional, amino acid and nucleotide levels. Conclusions/Significance Our results offer support for the hypothesis that “novel F genome-specific mitochondrial genes” are involved in key biological functions in bivalve species with DUI.
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Affiliation(s)
- Sophie Breton
- Kent State University, Kent, Ohio, United States of America.
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Soroka M, Burzyński A. Complete sequences of maternally inherited mitochondrial genomes in mussels Unio pictorum (Bivalvia, Unionidae). J Appl Genet 2011; 51:469-76. [PMID: 21063064 DOI: 10.1007/bf03208876] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondrial genomes are frequently used to infer phylogenetic relationships. Some taxa are, however, poorly represented. To facilitate better understanding of the potential of mitochondrial genome data in freshwater mussels, we present here, for the first time, the mitochondrial sequences of 4 complete F-type mitochondrial genomes from the European freshwater bivalve Unio pictorum (Unionidae). These genomes are very compact (15,761 bp) but have a typical gene complement for bilaterian mitochondrial genomes and a very similar organization to other unionid genomes available in databases. Very low nucleotide diversity within the species suggests a small effective population size of Polish U. pictorum, a phenomenon of potential importance for environmental management policies.
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Affiliation(s)
- M Soroka
- University of Szczecin, Department of Genetics, Felczaka 3c, 71-412 Szczecin, Poland.
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Characteristics of mitochondrial DNA of unionid bivalves (Mollusca: Bivalvia: Unionidae). I. Detection and characteristics of doubly uniparental inheritance (DUI) of unionid mitochondrial DNA. FOLIA MALACOLOGICA 2011. [DOI: 10.2478/v10125-010-0015-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Breton S, Stewart DT, Shepardson S, Trdan RJ, Bogan AE, Chapman EG, Ruminas AJ, Piontkivska H, Hoeh WR. Novel protein genes in animal mtDNA: a new sex determination system in freshwater mussels (Bivalvia: Unionoida)? Mol Biol Evol 2010; 28:1645-59. [PMID: 21172831 DOI: 10.1093/molbev/msq345] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial (mt) function depends critically on optimal interactions between components encoded by mt and nuclear DNAs. mitochondrial DNA (mtDNA) inheritance (SMI) is thought to have evolved in animal species to maintain mito-nuclear complementarity by preventing the spread of selfish mt elements thus typically rendering mtDNA heteroplasmy evolutionarily ephemeral. Here, we show that mtDNA intraorganismal heteroplasmy can have deterministic underpinnings and persist for hundreds of millions of years. We demonstrate that the only exception to SMI in the animal kingdom, that is, the doubly uniparental mtDNA inheritance system in bivalves, with its three-way interactions among egg mt-, sperm mt- and nucleus-encoded gene products, is tightly associated with the maintenance of separate male and female sexes (dioecy) in freshwater mussels. Specifically, this mother-through-daughter and father-through-son mtDNA inheritance system, containing highly differentiated mt genomes, is found in all dioecious freshwater mussel species. Conversely, all hermaphroditic species lack the paternally transmitted mtDNA (=possess SMI) and have heterogeneous macromutations in the recently discovered, novel protein-coding gene (F-orf) in their maternally transmitted mt genomes. Using immunoelectron microscopy, we have localized the F-open reading frame (ORF) protein, likely involved in specifying separate sexes, in mitochondria and in the nucleus. Our results support the hypothesis that proteins coded by the highly divergent maternally and paternally transmitted mt genomes could be directly involved in sex determination in freshwater mussels. Concomitantly, our study demonstrates novel features for animal mt genomes: the existence of additional, lineage-specific, mtDNA-encoded proteins with functional significance and the involvement of mtDNA-encoded proteins in extra-mt functions. Our results open new avenues for the identification, characterization, and functional analyses of ORFs in the intergenic regions, previously defined as "noncoding," found in a large proportion of animal mt genomes.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, Kent State University, Kent, OH, USA.
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Doucet-Beaupré H, Breton S, Chapman EG, Blier PU, Bogan AE, Stewart DT, Hoeh WR. Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA. BMC Evol Biol 2010; 10:50. [PMID: 20167078 PMCID: PMC2834691 DOI: 10.1186/1471-2148-10-50] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/18/2010] [Indexed: 11/10/2022] Open
Abstract
Background Doubly uniparental inheritance (DUI) is an atypical system of animal mtDNA inheritance found only in some bivalves. Under DUI, maternally (F genome) and paternally (M genome) transmitted mtDNAs yield two distinct gender-associated mtDNA lineages. The oldest distinct M and F genomes are found in freshwater mussels (order Unionoida). Comparative analyses of unionoid mitochondrial genomes and a robust phylogenetic framework are necessary to elucidate the origin, function and molecular evolutionary consequences of DUI. Herein, F and M genomes from three unionoid species, Venustaconcha ellipsiformis, Pyganodon grandis and Quadrula quadrula have been sequenced. Comparative genomic analyses were carried out on these six genomes along with two F and one M unionoid genomes from GenBank (F and M genomes of Inversidens japanensis and F genome of Lampsilis ornata). Results Compared to their unionoid F counterparts, the M genomes contain some unique features including a novel localization of the trnH gene, an inversion of the atp8-trnD genes and a unique 3'coding extension of the cytochrome c oxidase subunit II gene. One or more of these unique M genome features could be causally associated with paternal transmission. Unionoid bivalves are characterized by extreme intraspecific sequence divergences between gender-associated mtDNAs with an average of 50% for V. ellipsiformis, 50% for I. japanensis, 51% for P. grandis and 52% for Q. quadrula (uncorrected amino acid p-distances). Phylogenetic analyses of 12 protein-coding genes from 29 bivalve and five outgroup mt genomes robustly indicate bivalve monophyly and the following branching order within the autolamellibranch bivalves: ((Pteriomorphia, Veneroida) Unionoida). Conclusion The basal nature of the Unionoida within the autolamellibranch bivalves and the previously hypothesized single origin of DUI suggest that (1) DUI arose in the ancestral autolamellibranch bivalve lineage and was subsequently lost in multiple descendant lineages and (2) the mitochondrial genome characteristics observed in unionoid bivalves could more closely resemble the DUI ancestral condition. Descriptions and comparisons presented in this paper are fundamental to a more complete understanding regarding the origins and consequences of DUI.
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Affiliation(s)
- Hélène Doucet-Beaupré
- Département de Biologie, Université du Québec à Rimouski, Rimouski, Québec, G5L 3A1, Canada .
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Mock KE, Box JCB, Chong JP, Howard JK, Nez DA, Wolf D, Gardner RS. Genetic structuring in the freshwater mussel Anodonta corresponds with major hydrologic basins in the western United States. Mol Ecol 2010; 19:569-91. [PMID: 20070523 DOI: 10.1111/j.1365-294x.2009.04468.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Freshwater mussels (unionids) are increasingly recognized as important providers of ecosystem services, yet are among the most endangered fauna in the world. Because unionids are generally sessile and require specific fish hosts for development and dispersal, they are particularly vulnerable to habitat degradation. Surprisingly, little is known about the distribution of genetic diversity in freshwater mussels and this gap has a negative impact on taxonomy, monitoring, conservation and ecological research in these species. Here, we focus on western North American Anodonta, one of only three genera known to exist in this broad landscape and which contains three highly divergent lineages. We describe phylogeographical subdivision in the most widespread and diverse of these lineages, which includes Anodonta californiensis and Anodonta nuttalliana and occurs from Canada to Mexico. Using mitochondrial and nuclear data, we found that genetic structuring within this clade is inconsistent with morphologically based species designations, but instead follows patterns of vicariance among major hydrogeologic basins. Furthermore, there was a strong tendency for population diversity within drainage systems to increase downstream, implying greater habitat or host fish availability in this direction. Microsatellite results indicated that sampling locations were all genetically distinct, even at short distances. Many of our sample populations showed evidence of a recent demographic bottleneck, although this effect seemed to be very local and not drainage or basin-specific. This study provides a foundation for the establishment of appropriate management units and future research on adaptive differentiation and host fish relationships.
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Affiliation(s)
- Karen E Mock
- Department of Wildland Resources, Utah State University, Logan, UT 84322-5230, USA.
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Soroka M. Identification of gender-associated mitochondrial haplotypes in Anodonta anatina (Bivalvia: Unionidae). FOLIA MALACOLOGICA 2009. [DOI: 10.12657/folmal.016.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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The control region of maternally and paternally inherited mitochondrial genomes of three species of the sea mussel genus Mytilus. Genetics 2009; 181:1045-56. [PMID: 19139146 DOI: 10.1534/genetics.108.093229] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species of the mussel genus Mytilus possess maternally and paternally transmitted mitochondrial genomes. In the interbreeding taxa Mytilus edulis and M. galloprovincialis, several genomes of both types have been fully sequenced. The genome consists of the coding part (which, in addition to protein and RNA genes, contains several small noncoding sequences) and the main control region (CR), which in turn consists of three distinct parts: the first variable (VD1), the conserved (CD), and the second variable (VD2) domain. The maternal and paternal genomes are very similar in gene content and organization, even though they differ by >20% in primary sequence. They differ even more at VD1 and VD2, yet they are remarkably similar at CD. The complete sequence of a genome from the closely related species M. trossulus was previously reported and found to consist of a maternal-like coding part and a paternal-like and a maternal-like CR. From this and from the fact that it was extracted from a male individual, it was inferred that this is a genome that switched from maternal to paternal transmission. Here we provide clear evidence that this genome is the maternal genome of M. trossulus. We have found that in this genome the tRNA(Gln) in the coding region is apparently defective and that an intact copy of this tRNA occurs in the CR, that one of the two conserved domains is missing essential motifs, and that one of the two first variable domains has a high rate of divergence. These features may explain the large size and mosaic structure of the CR of the maternal genome of M. trossulus. We have also obtained CR sequences of the maternal and paternal genomes of M. californianus, a more distantly related species. We compare the control regions from all three species, focusing on the divergence among genomes of different species origin and among genomes of different transmission routes.
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Masculinization Events and Doubly Uniparental Inheritance of Mitochondrial DNA: A Model for Understanding the Evolutionary Dynamics of Gender-Associated mtDNA in Mussels. Evol Biol 2009. [DOI: 10.1007/978-3-642-00952-5_9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Filipowicz M, Burzyński A, Śmietanka B, Wenne R. Recombination in Mitochondrial DNA of European Mussels Mytilus. J Mol Evol 2008; 67:377-88. [DOI: 10.1007/s00239-008-9157-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Revised: 07/08/2008] [Accepted: 08/05/2008] [Indexed: 10/21/2022]
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CAMPBELL DAVIDC, JOHNSON PAULD, WILLIAMS JAMESD, RINDSBERG ANDREWK, SERB JEANNEM, SMALL KORYK, LYDEARD CHARLES. Identification of ‘extinct’ freshwater mussel species using DNA barcoding. Mol Ecol Resour 2008; 8:711-24. [DOI: 10.1111/j.1755-0998.2008.02108.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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