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      The mitochondrial genomes of five frog species of the Neotropical genus Ischnocnema (Anura: Brachycephaloidea: Brachycephalidae)

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          Abstract

          We report the mitogenomes for five species of the Ischnocnema guentheri series, being the first described for this genus of brachycephalid frogs. We assembled mitogenomes from anchored hybrid enrichment data and recovered the 13 protein-coding genes, 22 tRNA genes, and two rRNA genes for all species. The general structure agrees with most previously sequenced neobatrachians, with two exceptions: the origin of replication of L-strand (O L) was found between tRNA-A and tRNA-N, and the position of tRNA-L and tRNA-T, which are dispersed in the control region. We provide a phylogenetic tree with outgroups, which is consistent with previous phylogenetic hypotheses.

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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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            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

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                17 August 2018
                2018
                : 3
                : 2
                : 915-917
                Affiliations
                [a ]Department of Zoology and Aquaculture Center (CAUNESP), Biosciences Institute, São Paulo State University – UNESP , Rio Claro, Brazil;
                [b ]Department of Zoology, Instituto de Biologia Roberto Alcântara Gomes, Rio de Janeiro State University – UERJ , Rio de Janeiro, Brazil;
                [c ]Department of Scientific Computing, Florida State University , Tallahassee, FL, USA;
                [d ]Department of Biological Science, Florida State University , Tallahasse, FL, USA;
                [e ]Zoological Institute Technical University of Braunschweig , Braunschweig, Germany
                Author notes

                Supplemental data for this article can be accessed here .

                CONTACT Pedro P. G. Taucce pedrotaucce@ 123456gmail.com Department of Zoology and Aquaculture Center (CAUNESP), Biosciences Institute, São Paulo State University – UNESP , Cx. Postal 199, 13506-569Rio Claro, SP, Brazil
                Author information
                https://orcid.org/0000-0002-3088-4543
                https://orcid.org/0000-0003-0747-0817
                https://orcid.org/0000-0002-7863-4965
                Article
                1501312
                10.1080/23802359.2018.1501312
                7800048
                833514ce-8e2a-4df6-95b0-709d32b0eb80
                © 2018 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.

                History
                Page count
                Figures: 1, Pages: 3, Words: 2414
                Categories
                Research Article
                Mitogenome Announcement

                amphibia,brazil,ischnocnema guentheri series,mitogenomes,terrarana

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