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      Complete mitochondrial genome of the Devil Ray, Mobula thurstoni (Lloyd, 1908) (Myliobatiformes: Myliobatidae)

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          Abstract

          The Devil Ray ( Mobula thurstoni) is a species with global distribution and is an important species in conservation terms, here we present its complete mitochondrial genome assembled with Illumina sequencing data. The circular genome was 17,610 bp in length, and consists of 13 protein-coding, two ribosomal RNAs (rRNAs), and 22 transfer RNA (tRNA) genes. Base composition is 30.7% A, 29.1% T, 26.5% C, and 13.7% G, and 40.2% GC content. Protein-coding genes present two start codon (ATG and GUG) and seven stop codon (UAA, AUA, UUU, UUA, AAU, CCU, and UAG). The control region possesses the highest A + T (66.6%) content among all mitochondrial regions. These data would contribute to the evolutionary studies of this genus, where there has been recent reclassification.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)
          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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            MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

            Koichiro Tamura, Glen Stecher, Daniel Walter Peterson … (2013)
            We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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              Quality control and preprocessing of metagenomic datasets

              Robert Schmieder, Robert Edwards (2011)
              Summary: Here, we present PRINSEQ for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets. Summary statistics of FASTA (and QUAL) or FASTQ files are generated in tabular and graphical form and sequences can be filtered, reformatted and trimmed by a variety of options to improve downstream analysis. Availability and Implementation: This open-source application was implemented in Perl and can be used as a stand alone version or accessed online through a user-friendly web interface. The source code, user help and additional information are available at http://prinseq.sourceforge.net/. Contact: rschmied@sciences.sdsu.edu; redwards@cs.sdsu.edu
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mitochondrial DNA B Resour
                Journal ID (iso-abbrev): Mitochondrial DNA B Resour
                Title: Mitochondrial DNA. Part B, Resources
                Publisher: Taylor & Francis
                ISSN (Electronic): 2380-2359
                Publication date (Electronic, pub): 26 November 2017
                Publication date (Electronic, collection): 2017
                Volume: 2
                Issue: 2
                Pages: 868-870
                Affiliations
                [a ]Facultad de Ciencias del Mar, Universidad Autónoma de Sinaloa , Mazatlán, Mexico;
                [b ]Unidad en Acuicultura y Manejo Ambiental, CONACyT-Centro de Investigación en Alimentación y Desarrollo A. C. , Mazatlán, Mexico;
                [c ]Centro Regional de investigaciones Pesqueras de Mazatlán, Instituto Nacional de Pesca , Mazatlán, Mexico;
                [d ]Instituto de Ciencias del Mar y Limnología, Unidad Academica Mazatlan, Universidad Nacional Autónoma de México , Mazatlán, Mexico;
                [e ]Facultad de Ciencias del Mar, CONACYT-Universidad Autónoma de Sinaloa , Mazatlán, Mexico
                Author notes
                CONTACT Nancy C. Saavedra-Sotelo nsaavedra@ 123456uas.edu.mx Facultad de Ciencias del Mar, CONACYT, UAS , Paseo Claussen s/n, Mazatlán, Sinaloa, C.P. 82000, Mexico
                Author information
                https://orcid.org/0000-0001-9873-9732
                https://orcid.org/0000-0001-9277-0675
                Article
                Publisher ID: 1407689
                DOI: 10.1080/23802359.2017.1407689
                PMC ID: 7800197
                SO-VID: 1799851d-bf37-44b9-9431-9bca2cb2ae70
                Copyright © © 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

                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.

                History
                Page count
                Figures: 1, Pages: 3, Words: 1645
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: ray,mobula,mitogenome,illumina
                Data availability:
                Keywords: ray, mobula, mitogenome, illumina

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