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The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida

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      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.

      Electronic supplementary material

      The online version of this article (10.1186/s12864-018-4583-3) contains supplementary material, which is available to authorized users.

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      Most cited references 73

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        The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
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            Author and article information

            Affiliations
            [1 ]ISNI 0000 0004 1936 9633, GRID grid.411959.1, Department of Biology, , Acadia University, ; Wolfville, NS Canada
            [2 ]ISNI 0000 0004 1936 8200, GRID grid.55602.34, Department of Biology, , Dalhousie University, ; Halifax, NS Canada
            [3 ]ISNI 0000 0001 2292 3357, GRID grid.14848.31, Département de Sciences Biologiques, , Université de Montréal, ; Montréal, QC, Canada
            Contributors
            emilychase@acadiau.ca
            brentrobicheau@acadiau.ca
            sr618131@dal.ca
            s.breton@umontreal.ca
            ORCID: http://orcid.org/0000-0002-4402-1757, don.stewart@acadiau.ca
            Journal
            BMC Genomics
            BMC Genomics
            BMC Genomics
            BioMed Central (London )
            1471-2164
            27 March 2018
            27 March 2018
            2018
            : 19
            29587633
            5870820
            4583
            10.1186/s12864-018-4583-3
            © The Author(s). 2018

            Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

            Funding
            Funded by: FundRef http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;
            Award ID: 217175
            Categories
            Research Article
            Custom metadata
            © The Author(s) 2018

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