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      Mitochondrial genomes of Anopheles arabiensis, An. gambiae and An. coluzzii show no clear species division

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          Abstract

          Here we report the complete mitochondrial sequences of 70 individual field collected mosquito specimens from throughout Sub-Saharan Africa. We generated this dataset to identify species specific markers for the following Anopheles species and chromosomal forms: An. arabiensis, An. coluzzii (The Forest and Mopti chromosomal forms) and An. gambiae (The Bamako and Savannah chromosomal forms).  The raw Illumina sequencing reads were mapped to the NC_002084 reference mitogenome sequence. A total of 783 single nucleotide polymorphisms (SNPs) were detected on the mitochondrial genome, of which 460 are singletons (58.7%). None of these SNPs are suitable as molecular markers to distinguish among An. arabiensis, An. coluzzii and An. gambiae or any of the chromosomal forms. The lack of species or chromosomal form specific markers is also reflected in the constructed phylogenetic tree, which shows no clear division among the operational taxonomic units considered here.

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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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            The variant call format and VCFtools

            Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk
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              Identification of single specimens of the Anopheles gambiae complex by the polymerase chain reaction.

              A ribosomal DNA-polymerase chain reaction (PCR) method has been developed for species identification of individuals of the five most widespread members of the Anopheles gambiae complex, a group of morphologically indistinguishable sibling mosquito species that includes the major vectors of malaria in Africa. The method, which is based on species-specific nucleotide sequences in the ribosomal DNA intergenic spacers, may be used to identify both species and interspecies hybrids, regardless of life stage, using either extracted DNA or fragments of a specimen. Intact portions of a mosquito as small as an egg or the segment of one leg may be placed directly into the PCR mixture for amplification and analysis. The method uses a cocktail of five 20-base oligonucleotides to identify An. gambiae, An. arabiensis, An. quadriannnulatus, and either An. melas in western Africa or An. melas in eastern and southern Africa.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal AnalysisRole: Writing – Original Draft PreparationRole: Writing – Review & Editing
                Role: Writing – Original Draft Preparation
                Role: Data CurationRole: Software
                Role: Investigation
                Role: Investigation
                Role: Writing – Review & Editing
                Role: InvestigationRole: Writing – Review & Editing
                Role: ConceptualizationRole: Data CurationRole: Formal AnalysisRole: Writing – Original Draft PreparationRole: Writing – Review & Editing
                Journal
                F1000Res
                F1000Res
                F1000Research
                F1000Research
                F1000 Research Limited (London, UK )
                2046-1402
                15 March 2019
                2018
                : 7
                Affiliations
                [1 ]Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis , Davis, CA, 95616, USA
                [2 ]Malaria Research and Training Center, University of Bamako, Bamako, E2528, Mali
                [3 ]Mosquito Control Research Laboratory, Kearney Agricultural Center, Department of Entomology and Nematology, University of California Davis, Davis, CA, 93648, USA
                [1 ]Department of Epidemiology, Faculty of Public Health, University of São Paulo, São Paulo, Brazil
                [1 ]Department of Epidemiology, Faculty of Public Health, University of São Paulo, São Paulo, Brazil
                [1 ]Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
                [2 ]Department of Public Health & Infectious Diseases, Sapienza University of Rome, Rome, Italy
                Author notes

                No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Article
                10.12688/f1000research.13807.2
                6489993
                Copyright: © 2019 Hanemaaijer MJ et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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                Funding
                Funded by: University of California Irvine Malaria Initiative
                We thank University of California - Irvine, Malaria Initiatives (UCIMI) for their support.
                The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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