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      Mitochondrial genome and phylogenetic analysis of Psylliodes punctifrons Baly (Coleoptera: Chrysomelidae: Galerucinae)

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      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Mitogenome, Psylliodes punctifrons, agricultural pest

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          Abstract

          We sequenced and annotated mitochondrial genome (mitogenome) of oilseed rape pest Psylliodes punctifrons Baly for the first time. The mitogenome is 15,611 bp, and the nucleotide composition of 37 genes is highly A + T biased (A: 34.2, C: 11.6, G: 12.1, and T:42.1). All PCGs start with ATN and stop with TAR, except COX3 and ND4 that stop with incomplete codon T—. The phylogenetic tree confirms that P. punctifrons is clustered with other Psylliodes species. This study enriches the mitogenomes of agricultural pests.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          Kazutaka Katoh, Daron Standley (2013)
          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.

            Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
            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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              MITOS: improved de novo metazoan mitochondrial genome annotation.

              Matthias Bernt, Alexander Donath, Frank Jühling … (2013)
              About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mitochondrial DNA B Resour
                Journal ID (iso-abbrev): Mitochondrial DNA B Resour
                Title: Mitochondrial DNA. Part B, Resources
                Publisher: Taylor & Francis
                ISSN (Electronic): 2380-2359
                Publication date (Electronic, pub): 27 October 2020
                Publication date (Electronic, collection): 2020
                Volume: 5
                Issue: 3
                Pages: 3631-3632
                Affiliations
                Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture, Institute of Entomology, Guizhou University , Guiyang, P. R. China
                Author notes
                CONTACT Chao-Xing Hu lihongwu2020@ 123456126.com Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture, Institute of Entomology, Guizhou University , Guiyang550025, P. R. China
                Article
                Publisher ID: 1832597
                DOI: 10.1080/23802359.2020.1832597
                PMC ID: 7594853
                SO-VID: c0aa6f26-7a80-420f-99a6-41dc7a4bcc80
                Copyright © © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

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

                History
                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 962
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: mitogenome,psylliodes punctifrons,agricultural pest
                Data availability:
                Keywords: mitogenome, psylliodes punctifrons, agricultural pest

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