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      The complete mitogenome of Lasioglossum affine (Hymenoptera: Halictidae) and phylogenetic analysis

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      Author(s): a , b , a , b , b , b , a , b , a , b
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Lasioglossum affine, Hymenoptera, mitogenome, phylogeny

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          Abstract

          The complete mitogenome of Lasioglossum affine (Hymenoptera: Halictidae) was sequenced and analyzed. The whole mitogenome is 17,352 bp (AT%=84.1%) and encodes 37 typical eukaryotic mitochondrial genes, including 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and an AT-rich region. Further analysis found three gene rearrangements, where trn I-Q-M →  trn M-I-Q, trn W-C-Y →  trn C-W-Y, and trn K-D →  trn D-K were shuffled. The phylogenetic relationships of 19 species of Hymenoptera were established using maximum-likelihood method based on 13 concatenated PCGs. The result showed that Lasioglossum affine is a sister of Lasioglossum sp. SJW-2017.

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)
          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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            SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

            Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)
            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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              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): 20 November 2020
                Publication date (Electronic, collection): 2020
                Volume: 5
                Issue: 3
                Pages: 3784-3785
                Affiliations
                [a ]Chongqing Key Laboratory of Vector Insects, Chongqing Normal University , Chongqing, China
                [b ]College of Life Sciences, Chongqing Normal University , Chongqing, China
                Author notes
                CONTACT Bo Li libcell@ 123456cqnu.edu.cn Chongqing Key Laboratory of Vector Insects, Chongqing Normal University , Chongqing, China
                Author information
                https://orcid.org/0000-0002-5416-0515
                https://orcid.org/0000-0002-5594-7168
                https://orcid.org/0000-0002-7706-4032
                https://orcid.org/0000-0001-9944-0003
                Article
                Publisher ID: 1835573
                DOI: 10.1080/23802359.2020.1835573
                PMC ID: 7682738
                PubMed ID: 33367102
                SO-VID: 0a955b1c-2968-4204-b017-4b0070fe3613
                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: 1220
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: lasioglossum affine,hymenoptera,mitogenome,phylogeny
                Data availability:
                Keywords: lasioglossum affine, hymenoptera, mitogenome, phylogeny

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