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      The complete mitochondrial genome of Dermacentor ( Indocentor) auratus (Acari, Ixodidae) Translated title: Le génome mitochondrial complet de Dermacentor ( Indocentor) auratus (Acari, Ixodidae)

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      Parasite

      EDP Sciences

      Dermacentor (Indocentor) auratus, Mitochondrial genome, Long-range PCR, Illumina sequencing

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          Abstract

          Dermacentor ( Indocentor) auratus Supino, 1897 is a prominent ixodid vector of numerous pathogens of public health and veterinary importance. Using long-range PCR of two overlapping regions sequenced on an Illumina MiSeq machine, the complete mitochondrial genome of D. auratus is reported here. The resulting contigs were able to be assembled into a complete and circularised genome which had the general organisation of the mitochondrial genomes of the Metastriates. It had a total length of 14,766 bp and contained 37 genes, including 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes, as well as 2 non-coding control regions and 3 tick-boxes. The phylogenetic analysis on the whole mitogenome confirmed the position of D. auratus within the Dermacentor clade.

          Translated abstract

          Dermacentor ( Indocentor) auratus Supino, 1897 est un ixode, vecteur notable de nombreux pathogènes importants en santé publique et en médecine vétérinaire. Utilisant la PCR en fragment long sur deux régions chevauchantes combinée au séquençage sur une plate-forme Illumina MiSeq, le génome mitochondrial complet de D. auratus est présenté ici. Les contigs obtenus ont été assemblés en un génome circulaire complet conforme à l’organisation générale des génomes mitochondriaux des Métastriates. D’une longueur totale de 14766 pb, il contient 37 gènes, incluant 13 gènes codants des protéines, 22 gènes d’ARN de transfert et 2 gènes d’ARN ribosomaux, ainsi que 2 régions contrôles non-codantes et 3 motifs « tick-box ». L’analyse phylogénétique sur le mitogénome complet confirme la position de D. auratus au sein du clade Dermacentor.

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          Most cited references 33

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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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            MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

            The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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              SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

              The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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                Author and article information

                Journal
                Parasite
                Parasite
                parasite
                Parasite
                EDP Sciences
                1252-607X
                1776-1042
                2021
                19 January 2021
                : 28
                : ( publisher-idID: parasite/2021/01 )
                Affiliations
                National Public Health Laboratory, National Centre for Infectious Diseases Block G, Level 13, 16 Jalan Tan Tock Seng Singapore 308442 Singapore
                Author notes
                [* ]Corresponding author: jmg_chavatte@ 123456ncid.sg
                Article
                parasite200157 10.1051/parasite/2021002
                10.1051/parasite/2021002
                7814750
                33464203
                © J.-M. Chavatte & S. Octavia, published by EDP Sciences, 2021

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

                Page count
                Figures: 3, Tables: 1, Equations: 0, References: 29, Pages: 7
                Categories
                Research Article

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