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      Characterization of the complete mitogenome of Anopheles aquasalis, and phylogenetic divergences among Anopheles from diverse geographic zones

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          Abstract

          Whole mitogenome sequences (mtDNA) have been exploited for insect ecology studies, using them as molecular markers to reconstruct phylogenies, or to infer phylogeographic relationships and gene flow. Recent Anopheles phylogenomic studies have provided information regarding the time of deep lineage divergences within the genus. Here we report the complete 15,393 bp mtDNA sequences of Anopheles aquasalis, a Neotropical human malaria vector. When comparing its structure and base composition with other relevant and available anopheline mitogenomes, high similarity and conserved genomic features were observed. Furthermore, 22 mtDNA sequences comprising anopheline and Dipteran sibling species were analyzed to reconstruct phylogenies and estimate dates of divergence between taxa. Phylogenetic analysis using complete mtDNA sequences suggests that A. aquasalis diverged from the Anopheles albitarsis complex ~28 million years ago (MYA), and ~38 MYA from Anopheles darlingi. Bayesian analysis suggests that the most recent ancestor of Nyssorhynchus and Anopheles + Cellia was extant ~83 MYA, corroborating current estimates of ~79–100 MYA. Additional sampling and publication of African, Asian, and North American anopheline mitogenomes would improve the resolution of the Anopheles phylogeny and clarify early continental dispersal routes.

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          TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

          We present TranslatorX, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations. Many comparisons between biological sequences (nucleic acids and proteins) involve the construction of multiple alignments. Alignments represent a statement regarding the homology between individual nucleotides or amino acids within homologous genes. As protein-coding DNA sequences evolve as triplets of nucleotides (codons) and it is known that sequence similarity degrades more rapidly at the DNA than at the amino acid level, alignments are generally more accurate when based on amino acids than on their corresponding nucleotides. TranslatorX novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs; (iii) translation of ambiguous codons when possible; (iv) an innovative criterion to clean nucleotide alignments with GBlocks based on protein information; and (v) a rich output, including Jalview-powered graphical visualization of the alignments, codon-based alignments coloured according to the corresponding amino acids, measures of compositional bias and first, second and third codon position specific alignments. The TranslatorX server is freely available at http://translatorx.co.uk.
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            Artemis: sequence visualization and annotation

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              The dominant Anopheles vectors of human malaria in Africa, Europe and the Middle East: occurrence data, distribution maps and bionomic précis

              Background This is the second in a series of three articles documenting the geographical distribution of 41 dominant vector species (DVS) of human malaria. The first paper addressed the DVS of the Americas and the third will consider those of the Asian Pacific Region. Here, the DVS of Africa, Europe and the Middle East are discussed. The continent of Africa experiences the bulk of the global malaria burden due in part to the presence of the An. gambiae complex. Anopheles gambiae is one of four DVS within the An. gambiae complex, the others being An. arabiensis and the coastal An. merus and An. melas. There are a further three, highly anthropophilic DVS in Africa, An. funestus, An. moucheti and An. nili. Conversely, across Europe and the Middle East, malaria transmission is low and frequently absent, despite the presence of six DVS. To help control malaria in Africa and the Middle East, or to identify the risk of its re-emergence in Europe, the contemporary distribution and bionomics of the relevant DVS are needed. Results A contemporary database of occurrence data, compiled from the formal literature and other relevant resources, resulted in the collation of information for seven DVS from 44 countries in Africa containing 4234 geo-referenced, independent sites. In Europe and the Middle East, six DVS were identified from 2784 geo-referenced sites across 49 countries. These occurrence data were combined with expert opinion ranges and a suite of environmental and climatic variables of relevance to anopheline ecology to produce predictive distribution maps using the Boosted Regression Tree (BRT) method. Conclusions The predicted geographic extent for the following DVS (or species/suspected species complex*) is provided for Africa: Anopheles (Cellia) arabiensis, An. (Cel.) funestus*, An. (Cel.) gambiae, An. (Cel.) melas, An. (Cel.) merus, An. (Cel.) moucheti and An. (Cel.) nili*, and in the European and Middle Eastern Region: An. (Anopheles) atroparvus, An. (Ano.) labranchiae, An. (Ano.) messeae, An. (Ano.) sacharovi, An. (Cel.) sergentii and An. (Cel.) superpictus*. These maps are presented alongside a bionomics summary for each species relevant to its control.
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                Author and article information

                Contributors
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                Role: Formal analysis
                Role: ConceptualizationRole: Formal analysisRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                3 September 2019
                2019
                : 14
                : 9
                : e0219523
                Affiliations
                [1 ] Laboratory of Medical Entomology, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
                [2 ] Biosystems Informatics and Genomics Group, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
                [3 ] Laboratory of Physiology of Haematophagous Insects, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
                [4 ] Daniel K. Inouye US Pacific Basin Agricultural Research Center (PBARC), United States Department of Agriculture, Agricultural Research Service, Hilo, Hawaii, United States of America
                [5 ] Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
                [6 ] Davis Arbovirus Research and Training, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
                [7 ] Institute of Clinical Research Borborema, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
                [8 ] Graduation Program in Tropical Medicine, Amazonas State University, Manaus, AM, Brazil
                [9 ] Foundation of Tropical Medicine Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
                [10 ] Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
                [11 ] Institute Leonidas and Maria Deane, Oswaldo Cruz Foundation, FIOCRUZ, Manaus, AM, Brazil
                Virginia Polytechnic Institute and State University, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-8564-2023
                http://orcid.org/0000-0002-0158-2482
                Article
                PONE-D-19-08753
                10.1371/journal.pone.0219523
                6720026
                31479460
                3c2fabf2-2986-4c73-8ade-f16de0968af6
                © 2019 Martinez-Villegas et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 17 April 2019
                : 25 June 2019
                Page count
                Figures: 4, Tables: 2, Pages: 22
                Funding
                This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley - USA supported by NIH S10 OD018174 Instrumentation Grant. The following Brazilian agencies partially funded this study: Fundação do Instituto Oswaldo Cruz (FIOCRUZ – PAPES VI); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Coordenaçao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES); Institutos Nacionais de Ciência e Tecnologia (INCTs Entomologia Molecular e Elimina Malária); Fundações de Amparo à Pesquisa dos Estados de Minas Gerais e Amazonas (FAPEMIG and FAPEAM). LMV was a Ph.D. student supported by the Programa de Estudantes - Convênio de Pos-Graduação (PEC-PG - CAPES). GCL was a fellow sponsored by Programme Science without Borders (CAPES); PFPP, NFCS, and WMM are research fellows supported by CNPq.
                Categories
                Research Article
                Medicine and Health Sciences
                Infectious Diseases
                Disease Vectors
                Insect Vectors
                Mosquitoes
                Biology and Life Sciences
                Species Interactions
                Disease Vectors
                Insect Vectors
                Mosquitoes
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Arthropoda
                Insects
                Mosquitoes
                Medicine and Health Sciences
                Infectious Diseases
                Disease Vectors
                Insect Vectors
                Mosquitoes
                Anopheles Gambiae
                Biology and Life Sciences
                Species Interactions
                Disease Vectors
                Insect Vectors
                Mosquitoes
                Anopheles Gambiae
                Biology and Life Sciences
                Organisms
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                Custom metadata
                The data underlying the results of this study are available in the NCBI Database as part of the Anopheles aquasalis whole genome shotgun sequencing project; accession number: NJHH00000000.

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