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      The second complete mitochondrial genome of Alphitobius diaperinus Panzer, 1797 (Coleoptera: Tenebrionidae): investigation of intraspecific variations on mitochondrial genome

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          Abstract

          We have determined the second mitochondrial genome of Alphitobius diaperinus Panzer, 1797 collected in Gyeonggi-do, Republic of Korea. The circular mitogenome of A. diaperinus is 15,512 bp long which is slightly longer than that of the previous mitogenome of A. diaperinus. It includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNAs. The base composition was AT-biased (72.4%). Intraspecific variation between two mitogenome of A. diaperinus was investigated: one SNP and one INDEL were identified, presenting the low level of intraspecific variations on mitochondrial genome.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)
          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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            The Sequence Alignment/Map format and SAMtools

            Heng Li, Bob Handsaker, Alec Wysoker … (2009)
            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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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.
              Article 0 comments Cited 8935 times – based on 0 reviews     Review now
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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): 23 July 2020
                Publication date (Electronic, collection): 2020
                Volume: 5
                Issue: 3
                Pages: 2979-2981
                Affiliations
                [a ]Department of Plant Medicine, Sunchon National University , Suncheon, Republic of Korea
                [b ]Department of Plant Medicine, Gyeongsang National University , Jinju, Republic of Korea
                [c ]InfoBoss Inc ., Seoul, Republic of Korea
                [d ]InfoBoss Research Center , Seoul, Republic of Korea
                [e ]Institute of Agriculture and Life Science, Gyeongsang National University , Jinju, Republic of Korea
                Author notes
                CONTACT Jongsun Park starflr@ 123456infoboss.co.kr InfoBoss Inc ., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea; InfoBoss Research Center , 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea;
                Wonhoon Lee wonhoon@ 123456gnu.ac.kr Department of Plant Medicine, Gyeongsang National University , Jinju, Republic of Korea; Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Republic of Korea
                Author information
                https://orcid.org/0000-0003-0786-4701
                Article
                Publisher ID: 1797575
                DOI: 10.1080/23802359.2020.1797575
                PMC ID: 7783036
                SO-VID: 8046be44-b369-4fe8-9451-ddcdd8853c69
                Copyright statement: © 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: 3, Words: 1681
                Product
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: mitochondrial genome,alphitobius diaperinus,coleoptera,intraspecific variations,south korea
                Data availability:
                Keywords: mitochondrial genome, alphitobius diaperinus, coleoptera, intraspecific variations, south korea

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