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      Phylogenomics reveals the history of host use in mosquitoes

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          Abstract

          Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: 188–250 MYA]), considerably older than previous estimates. Moreover, we utilize an extensive database of host associations for mosquitoes to show that mosquitoes have shifted to feeding upon the blood of mammals numerous times, and that mosquito diversification and host-use patterns within major lineages appear to coincide in earth history both with major continental drift events and with the diversification of vertebrate classes.

          Abstract

          Despite the significance of mosquitos for human health, little research has focused on their phylogeny. Here, the authors present a resolved phylogenetic history of mosquitoes based on phylogenomics showing that these major disease vectors radiated coincidentally with geologic events and the diversification of their hosts.

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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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              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

                Contributors
                bwiegman@ncsu.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                6 October 2023
                6 October 2023
                2023
                : 14
                : 6252
                Affiliations
                [1 ]Department of Entomology and Plant Pathology, North Carolina State University, ( https://ror.org/04tj63d06) Raleigh, NC USA
                [2 ]Faculty of Veterinary Medicine, University of Calgary, ( https://ror.org/03yjb2x39) Calgary, AB Canada
                [3 ]GRID grid.1214.6, ISNI 0000 0000 8716 3312, Walter Reed Biosystematics Unit, , Smithsonian Institution Museum Support Center, ; Suitland, MD USA
                [4 ]One Health Branch, Walter Reed Army Institute of Research, ( https://ror.org/0145znz58) Silver Spring, MD USA
                [5 ]GRID grid.453560.1, ISNI 0000 0001 2192 7591, Department of Entomology, , Smithsonian Institution National Museum of Natural History, ; Washington, DC USA
                [6 ]Center for Vector-Borne Diseases, University of Texas Rio Grande Valley, ( https://ror.org/02p5xjf12) Edinburg, TX USA
                [7 ]Department of Biology, Clark University, ( https://ror.org/04123ky43) Worcester, MA USA
                [8 ]Department of Ecology and Evolutionary Biology, Yale University, ( https://ror.org/03v76x132) New Haven, CT USA
                [9 ]Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, ( https://ror.org/02t7c5797) New Haven, CT USA
                [10 ]Bohart Museum of Entomology, University of California, ( https://ror.org/05t99sp05) Davis, CA USA
                [11 ]GRID grid.469914.7, ISNI 0000 0004 0385 5215, CSIRO Land and Water, ; Canberra, ACT Australia
                [12 ]GRID grid.15276.37, ISNI 0000 0004 1936 8091, Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, , University of Florida, ; Vero Beach, FL USA
                [13 ]Department of Applied Ecology, North Carolina State University, ( https://ror.org/04tj63d06) Raleigh, NC USA
                [14 ]GRID grid.1016.6, ISNI 0000 0001 2173 2719, Australian National Insect Collection, , CSIRO National Collections and Marine Infrastructure, ; Canberra, ACT Australia
                [15 ]Departamento de Epidemiologia, Faculdade de Saude Publica, Universidade de Sao Paulo, ( https://ror.org/036rp1748) Sao Paulo, Brazil
                [16 ]College of Health and Human Sciences, School of Health Sciences, Western Carolina University, ( https://ror.org/010h78f45) Cullowhee, NC USA
                [17 ]Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, ( https://ror.org/02wb73912) San Francisco, CA USA
                Author information
                http://orcid.org/0000-0003-4469-2072
                http://orcid.org/0000-0003-2387-8214
                http://orcid.org/0000-0001-6168-1637
                http://orcid.org/0000-0003-3968-8124
                http://orcid.org/0000-0001-6366-1357
                http://orcid.org/0000-0001-7729-6143
                http://orcid.org/0000-0002-7051-2891
                http://orcid.org/0000-0002-1869-9759
                Article
                41764
                10.1038/s41467-023-41764-y
                10558525
                37803007
                bc252d16-68cc-488f-8296-0afaf149dfb1
                © Springer Nature Limited 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 25 January 2023
                : 8 September 2023
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000155, NSF | BIO | Division of Environmental Biology (DEB);
                Award ID: DEB-7534376
                Award Recipient :
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                © Springer Nature Limited 2023

                Uncategorized
                phylogenetics,entomology,evolutionary genetics,genomics
                Uncategorized
                phylogenetics, entomology, evolutionary genetics, genomics

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