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Lubośny M, Śmietanka B, Arculeo M, Burzyński A. No evidence of DUI in the Mediterranean alien species Brachidontes pharaonis (P. Fisher, 1870) despite mitochondrial heteroplasmy. Sci Rep 2022; 12:8569. [PMID: 35595866 PMCID: PMC9122905 DOI: 10.1038/s41598-022-12606-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/13/2022] [Indexed: 01/05/2023] Open
Abstract
Two genetically different mitochondrial haplogroups of Brachidontes pharaonis (p-distance 6.8%) have been identified in the Mediterranean Sea. This hinted at a possible presence of doubly uniparental inheritance in this species. To ascertain this possibility, we sequenced two complete mitogenomes of Brachidontes pharaonis mussels and performed a qPCR analysis to measure the relative mitogenome copy numbers of both mtDNAs. Despite the presence of two very similar regions composed entirely of repetitive sequences in the two haplogroups, no recombination between mitogenomes was detected. In heteroplasmic individuals, both mitogenomes were present in the generative tissues of both sexes, which argues against the presence of doubly uniparental inheritance in this species.
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Marco Arculeo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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2
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Lubośny M, Przyłucka A, Śmietanka B, Burzyński A. Semimytilus algosus: first known hermaphroditic mussel with doubly uniparental inheritance of mitochondrial DNA. Sci Rep 2020; 10:11256. [PMID: 32647112 PMCID: PMC7347871 DOI: 10.1038/s41598-020-67976-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/11/2020] [Indexed: 11/08/2022] Open
Abstract
Doubly uniparental inheritance (DUI) of mitochondrial DNA is a rare phenomenon occurring in some freshwater and marine bivalves and is usually characterized by the mitochondrial heteroplasmy of male individuals. Previous research on freshwater Unionida mussels showed that hermaphroditic species do not have DUI even if their closest gonochoristic counterparts do. No records showing DUI in a hermaphrodite have ever been reported. Here we show for the first time that the hermaphroditic mussel Semimytilus algosus (Mytilida), very likely has DUI, based on the complete sequences of both mitochondrial DNAs and the distribution of mtDNA types between male and female gonads. The two mitogenomes show considerable divergence (34.7%). The presumably paternal M type mitogenome dominated the male gonads of most studied mussels, while remaining at very low or undetectable levels in the female gonads of the same individuals. If indeed DUI can function in the context of simultaneous hermaphroditism, a change of paradigm regarding its involvement in sex determination is needed. It is apparently associated with gonadal differentiation rather than with sex determination in bivalves.
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
| | - Aleksandra Przyłucka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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Lubośny M, Śmietanka B, Przyłucka A, Burzyński A. Highly divergent mitogenomes ofGeukensia demissa(Bivalvia, Mytilidae) with extreme AT content. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12354] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology Institute of Oceanology Polish Academy of Sciences Sopot Poland
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology Institute of Oceanology Polish Academy of Sciences Sopot Poland
| | - Aleksandra Przyłucka
- Department of Genetics and Marine Biotechnology Institute of Oceanology Polish Academy of Sciences Sopot Poland
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology Institute of Oceanology Polish Academy of Sciences Sopot Poland
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4
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Chacón GM, Arias‐Pérez A, Freire R, Martínez L, Nóvoa S, Naveira H, Insua A. Evidence of doubly uniparental inheritance of the mitochondrial
DNA
in
Polititapes rhomboides
(Bivalvia, Veneridae): Evolutionary and population genetic analysis of F and M mitotypes. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ginna M. Chacón
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Alberto Arias‐Pérez
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Ruth Freire
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Luisa Martínez
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Susana Nóvoa
- Centro de Cultivos Marinos de Ribadeo‐CIMAXunta de Galicia Ribadeo (Lugo) Spain
| | - Horacio Naveira
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Ana Insua
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
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5
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Śmietanka B, Lubośny M, Przyłucka A, Gérard K, Burzyński A. Mitogenomics of Perumytilus purpuratus (Bivalvia: Mytilidae) and its implications for doubly uniparental inheritance of mitochondria. PeerJ 2018; 6:e5593. [PMID: 30245933 PMCID: PMC6149501 DOI: 10.7717/peerj.5593] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/14/2018] [Indexed: 12/29/2022] Open
Abstract
Animal mitochondria are usually inherited through the maternal lineage. The exceptional system allowing fathers to transmit their mitochondria to the offspring exists in some bivalves. Its taxonomic spread is poorly understood and new mitogenomic data are needed to fill the gap. Here, we present for the first time the two divergent mitogenomes from Chilean mussel Perumytilus purpuratus. The existence of these sex-specific mitogenomes confirms that this species has the doubly uniparental inheritance (DUI) of mitochondria. The genetic distance between the two mitochondrial lineages in P. purpuratus is not only much bigger than in the Mytilus edulis species complex but also greater than the distance observed in Musculista senhousia, the only other DUI-positive member of the Mytilidae family for which both complete mitochondrial genomes were published to date. One additional, long ORF (open reading frame) is present exclusively in the maternal mitogenome of P. purpuratus. This ORF evolves under purifying selection, and will likely be a target for future DUI research.
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Affiliation(s)
- Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Aleksandra Przyłucka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Karin Gérard
- Centro de Investigacion Gaia-Antartica, Departamento de Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile.,Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Punta Arenas, Chile
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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Weydmann A, Przyłucka A, Lubośny M, Walczyńska KS, Serrão EA, Pearson GA, Burzyński A. Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non-coding regions. Sci Rep 2017; 7:13702. [PMID: 29057900 PMCID: PMC5651803 DOI: 10.1038/s41598-017-13807-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
We determined the nearly complete mitochondrial genomes of the Arctic Calanus glacialis and its North Atlantic sibling Calanus finmarchicus, which are key zooplankton components in marine ecosystems. The sequenced part of C. glacialis mitogenome is 27,342 bp long and consists of two contigs, while for C. finmarchicus it is 29,462 bp and six contigs, what makes them the longest reported copepod mitogenomes. The typical set of metazoan mitochondrial genes is present in these mitogenomes, although the non-coding regions (NCRs) are unusually long and complex. The mitogenomes of the closest species C. glacialis and C. finmarchicus, followed by the North Pacific C. sinicus, are structurally similar and differ from the much more typical of deep-water, Arctic C. hyperboreus. This evolutionary trend for the expansion of NCRs within the Calanus mitogenomes increases mitochondrial DNA density, what resulted in its similar density to the nuclear genome. Given large differences in the length and structure of C. glacialis and C. finmarchicus mitogenomes, we conclude that the species are genetically distinct and thus cannot hybridize. The molecular resources presented here: the mitogenomic and rDNA sequences, and the database of repetitive elements should facilitate the development of genetic markers suitable in pursuing evolutionary research in copepods.
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Affiliation(s)
- Agata Weydmann
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland.
- University of Gdansk, Institute of Oceanography, Gdynia, 81-378, Poland.
| | | | - Marek Lubośny
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland
| | | | - Ester A Serrão
- University of Algarve, CCMAR, CIMAR, Faro, 8005-139, Portugal
| | | | - Artur Burzyński
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland
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Ghiselli F, Milani L, Iannello M, Procopio E, Chang PL, Nuzhdin SV, Passamonti M. The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae). PeerJ 2017; 5:e3692. [PMID: 28848689 PMCID: PMC5571815 DOI: 10.7717/peerj.3692] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/25/2017] [Indexed: 12/30/2022] Open
Abstract
Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam. Ruditapes decussatus is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy. In this work we: (i) assembled Ruditapes decussatus mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii) analyzed and characterized the Ruditapes decussatus mitochondrial genome, comparing its features with those of other venerid bivalves; (iii) assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ∼100 bivalve species. According to our analyses, Ruditapes decussatus is more genetically similar to species of the Genus Paphia than to the congeneric Ruditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of Ruditapes decussatus is a cause or an effect of the ongoing replacement of Ruditapes decussatus with the invasive Ruditapes philippinarum, and more analyses, especially on nuclear sequences, are required to assess this point.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Emanuele Procopio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Peter L Chang
- Department of Biological Sciences, Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
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