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Capt C, Bouvet K, Guerra D, Robicheau BM, Stewart DT, Pante E, Breton S. Unorthodox features in two venerid bivalves with doubly uniparental inheritance of mitochondria. Sci Rep 2020; 10:1087. [PMID: 31974502 PMCID: PMC6978325 DOI: 10.1038/s41598-020-57975-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/09/2020] [Indexed: 12/02/2022] Open
Abstract
In animals, strictly maternal inheritance (SMI) of mitochondria is the rule, but one exception (doubly uniparental inheritance or DUI), marked by the transmission of sex-specific mitogenomes, has been reported in bivalves. Associated with DUI is a frequent modification of the mitochondrial cox2 gene, as well as additional sex-specific mitochondrial genes not involved in oxidative phosphorylation. With the exception of freshwater mussels (for 3 families of the order Unionida), these DUI-associated features have only been shown in few species [within Mytilidae (order Mytilida) and Veneridae (order Venerida)] because of the few complete sex-specific mitogenomes published for these orders. Here, we present the complete sex-specific mtDNAs of two recently-discovered DUI species in two families of the order Venerida, Scrobicularia plana (Semelidae) and Limecola balthica (Tellinidae). These species display the largest differences in genome size between sex-specific mitotypes in DUI species (>10 kb), as well as the highest mtDNA divergences (sometimes reaching >50%). An important in-frame insertion (>3.5 kb) in the male cox2 gene is partly responsible for the differences in genome size. The S. plana cox2 gene is the largest reported so far in the Kingdom Animalia. The mitogenomes may be carrying sex-specific genes, indicating that general mitochondrial features are shared among DUI species.
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Affiliation(s)
- Charlotte Capt
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada.
| | - Karim Bouvet
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada
| | - Davide Guerra
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada
| | | | - Donald T Stewart
- Department of Biology, Acadia University, Wolfville, NS, B4P 2R6, Canada
| | - Eric Pante
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - Sophie Breton
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada.
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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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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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Wen HB, Cao ZM, Hua D, Xu P, Ma XY, Jin W, Yuan XH, Gu RB. The Complete Maternally and Paternally Inherited Mitochondrial Genomes of a Freshwater Mussel Potamilus alatus (Bivalvia: Unionidae). PLoS One 2017; 12:e0169749. [PMID: 28068380 PMCID: PMC5222514 DOI: 10.1371/journal.pone.0169749] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/21/2016] [Indexed: 11/18/2022] Open
Abstract
Doubly uniparental inheritance (DUI) of mitochondrial DNA, found only in some bivalve families and characterized by the existence of gender-associated mtDNA lineages that are inherited through males (M-type) or females (F-type), is one of the very few exceptions to the general rule of strict maternal mtDNA inheritance in animals. M-type sequences are often undetected and hence still underrepresented in the GenBank, which hinders the progress of the understanding of the DUI phenomenon. We have sequenced and analyzed the complete M and F mitogenomes of a freshwater mussel, Potamilus alatus. The M-type was 493 bp longer (M = 16 560, F = 16 067 bp). Gene contents, order and the distribution of genes between L and H strands were typical for unionid mussels. Candidates for the two ORFan genes (forf and morf) were found in respective mitogenomes. Both mitogenomes had a very similar A+T bias: F = 61% and M = 62.2%. The M mitogenome-specific cox2 extension (144 bp) is much shorter than in other sequenced unionid mitogenomes (531-576 bp), which might be characteristic for the Potamilus genus. The overall topology of the phylogenetic tree is in very good agreement with the currently accepted phylogenetic relationships within the Unionidae: both studied sequences were placed within the Ambleminae subfamily clusters in the corresponding M and F clades.
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Affiliation(s)
- Hai B Wen
- Wuxi Fishery College, Nanjing Agriculture University, Jiangsu, China.,Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes-Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China.,Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China
| | - Zhe M Cao
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes-Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China
| | - Dan Hua
- Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China
| | - Pao Xu
- Wuxi Fishery College, Nanjing Agriculture University, Jiangsu, China.,Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes-Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China.,Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China
| | - Xue Y Ma
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes-Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China.,Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China
| | - Wu Jin
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes-Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China.,Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China
| | - Xin H Yuan
- Wuxi Fishery College, Nanjing Agriculture University, Jiangsu, China.,Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes-Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China.,Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China
| | - Ruo B Gu
- Wuxi Fishery College, Nanjing Agriculture University, Jiangsu, China.,Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes-Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China.,Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China
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