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      The Complete Maternally and Paternally Inherited Mitochondrial Genomes of a Freshwater Mussel Potamilus alatus (Bivalvia: Unionidae)

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          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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          Most cited references 34

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          Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

           S Altschul (1997)
          The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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            MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

            We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Affiliations
                [1 ]Wuxi Fishery College, Nanjing Agriculture University, Jiangsu, China
                [2 ]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
                [3 ]Sino-US Cooperative Laboratory for Germplasm Conservation and Utilization of Freshwater Mollusks, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu, China
                University of Cambridge, UNITED KINGDOM
                Author notes

                Competing Interests: The authors report no conflict of interest.

                • Conceptualization: HBW ZMC PX DH XHY RBG.

                • Formal analysis: HBW ZMC XYM WJ.

                • Funding acquisition: HBW PX RBG.

                • Investigation: HBW ZMC XYM WJ.

                • Methodology: HBW ZMC PX DH XHY RBG.

                • Project administration: HBW.

                • Resources: HBW ZMC DH XHY.

                • Supervision: PX RBG.

                • Validation: XYM WJ RBG.

                • Visualization: HBW ZMC.

                • Writing – original draft: HBW ZMC.

                • Writing – review & editing: HBW ZMC PX RBG.

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                9 January 2017
                2017
                : 12
                : 1
                PONE-D-16-30663
                10.1371/journal.pone.0169749
                5222514
                28068380
                © 2017 Wen et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Counts
                Figures: 3, Tables: 1, Pages: 12
                Product
                Funding
                Funded by: Special Scientific Research Funds for Central Non-profit Institutes of Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences; Fisheries Sanxin Engineering Funds of Ocean and Fishery Bureau of Jiangsu Province
                Award ID: 2015JBFM02, Y2014-38
                Award Recipient :
                This study was supported by the Special Scientific Research Funds for Central Non-profit Institutes of Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences (Grant number: 2015JBFM02), and Fisheries Sanxin Engineering Funds of Ocean and Fishery Bureau of Jiangsu Province (Grant number: Y2014-38). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and life sciences
                Genetics
                DNA
                Forms of DNA
                Mitochondrial DNA
                Biology and life sciences
                Biochemistry
                Nucleic acids
                DNA
                Forms of DNA
                Mitochondrial DNA
                Biology and Life Sciences
                Organisms
                Animals
                Invertebrates
                Molluscs
                Bivalves
                Earth Sciences
                Hydrology
                Fresh Water
                Research and Analysis Methods
                Database and Informatics Methods
                Biological Databases
                Genomic Databases
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Genomic Databases
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Genomic Databases
                Biology and Life Sciences
                Biochemistry
                Bioenergetics
                Energy-Producing Organelles
                Mitochondria
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Energy-Producing Organelles
                Mitochondria
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Alignment
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Phylogenetic Analysis
                Research and Analysis Methods
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Phylogenetic Analysis
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Computer and Information Sciences
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                Custom metadata
                Apart from the two genomic sequences, all relevant data are within the paper and its Supporting Information files. GenBank accession numbers for the two genomic sequences are KU559011 (F) and KU559010 (M). The two specimens used for the DNA extraction are stored at the Freshwater Fisheries Research Center, Department of Aquaculture, Wuxi, China, under accession numbers N120F (F) and N466M (M).

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