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      The complete mitochondrial genome of the fine flounder Paralichthys adspersus revealed by next-generation sequencing

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          Abstract

          The complete mitochondrial genome of the fine flounder Paralichthys adspersus, was determined for the first time through Next Generation Sequencing (NGS) approach. The mitogenome (GenBank accession no. MW288827) has 17,060 bp in length and consisted of the well-known 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and the control region. The overall nucleotide composition of the whole mitogenome was A: 27.5%, C: 29.5%, G: 17.1%, and T: 25.9%. Phylogenetic analyses based on 12 protein-coding genes clustered P. adspersus in the monophyletic Paralichthyidae clade, showing the closest phylogenetic relationship with its congeneric species P. olivaceus.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            jModelTest 2: more models, new heuristics and parallel computing.

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              MrBayes 3: Bayesian phylogenetic inference under mixed models.

              MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                31 August 2021
                2021
                31 August 2021
                : 6
                : 10
                : 2785-2787
                Affiliations
                [a ]Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa , Chimbote, Peru
                [b ]Laboratorio de Biología del Desarrollo, Instituto Tecnológico de Chascomús, INTECH (CONICET-UNSAM) , Chascomús, Argentina
                Author notes
                [*]

                Equal contribution.

                CONTACT Eliana Zelada-Mázmela ezelada@ 123456uns.edu.pe Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa , Chimbote, Peru
                Juan I. Fernandino fernandino@ 123456intech.gov.ar Laboratorio de Biología del Desarrollo, Instituto Tecnológico de Chascomús, INTECH (CONICET-UNSAM) , Chascomús, Argentina
                Author information
                https://orcid.org/0000-0003-1754-2802
                Article
                1914217
                10.1080/23802359.2021.1914217
                8425720
                9c53777a-b60b-4ee2-8926-41d9d915c928
                © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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                Page count
                Figures: 1, Tables: 0, Pages: 3, Words: 1278
                Categories
                Research Article
                Mitogenome Announcement

                mitogenome,paralichthyidae,flatfish,ngs,perú
                mitogenome, paralichthyidae, flatfish, ngs, perú

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