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      Mitogenomes provide new insights of evolutionary history of Boreheptagyiini and Diamesini (Diptera: Chironomidae: Diamesinae)

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          Abstract

          Mitogenomes have been widely used for phylogenetic reconstruction of various Dipteran groups, but specifically for chironomid, they have not been carried out to resolve the relationships. Diamesinae (Diptera: Chironomidae) are important bioindicators for freshwater ecosystem monitoring, but its evolutionary history remains uncertain for lack of information. Here, coupled with one previously published and 30 new mitogenomes of Diamesinae, we carried out comparative mitogenomic analysis and phylogenetic analysis. Mitogenomes of Diamesinae were conserved in structure, and all genes arranged in the same order as the ancestral insect mitogenome. All protein‐coding genes in Diamesinae were under stronger purifying selection than those of other nonbiting midge species, which may exhibit signs of adaptation to life at cold living conditions. Phylogenetic analyses strongly supported the monophyly of Diamesinae, with Boreheptagyiini deeply nested within Diamesini. In addition, phylogenetic relationship of selected six genera was resolved, except Sympotthastia remained unstable. Our study revealed that the mitogenomes of Diamesinae are highly conserved, and they are practically useful for phylogenetic inference.

          Abstract

          Here, coupled with one previously published and 30 new mitogenomes of Diamesinae, we carried out comparative mitogenomic analysis and phylogenetic analysis. Mitogenomes of Diamesinae were conserved in structure, and all genes arranged in the same order as the ancestral insect mitogenome. Phylogenetic analyses strongly supported the monophyly of Diamesinae, with Boreheptagyiini deeply nested within Diamesini.

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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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              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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                Author and article information

                Contributors
                chenguangzheng@nankai.edu.cn
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                24 May 2022
                May 2022
                : 12
                : 5 ( doiID: 10.1002/ece3.v12.5 )
                : e8957
                Affiliations
                [ 1 ] ringgold 12538; College of Life Sciences Nankai University Tianjin China
                [ 2 ] ringgold 74518; Geological Museum of China Beijing China
                [ 3 ] ringgold 12380; School of Ecology and Nature Conservation Beijing Forestry University Beijing China
                [ 4 ] ringgold 91633; Department of Plant Protection College of Horticulture and Landscape Tianjin Agricultural University Tianjin China
                Author notes
                [*] [* ] Correspondence

                Chen‐Guang Zheng, College of Life Sciences, Nankai University, Tianjin 300071, China.

                Email: chenguangzheng@ 123456nankai.edu.cn

                Author information
                https://orcid.org/0000-0001-6544-6204
                https://orcid.org/0000-0003-0484-6153
                Article
                ECE38957
                10.1002/ece3.8957
                9130564
                35646319
                00510403-01f5-42b4-a230-8d20adc60f80
                © 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 16 April 2022
                : 11 October 2021
                : 06 May 2022
                Page count
                Figures: 6, Tables: 1, Pages: 13, Words: 7449
                Funding
                Funded by: Technological Innovation Talent Training Project of the Ministry of Natural Resources of China
                Award ID: 12110600000018003910
                Funded by: National Natural Science Foundation of China , doi 10.13039/501100001809;
                Award ID: 31900344
                Award ID: 41502021
                Funded by: China Postdoctoral Science Foundation , doi 10.13039/501100002858;
                Award ID: 2018M640227
                Categories
                Evolutionary Ecology
                Research Article
                Research Articles
                Custom metadata
                2.0
                May 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.6 mode:remove_FC converted:25.05.2022

                Evolutionary Biology
                diamesinae,mitogenome,phylogeny
                Evolutionary Biology
                diamesinae, mitogenome, phylogeny

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