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      The complete mitochondrial genome of Ceutorhynchus obstrictus (Marsham, 1802) (Coleoptera: Curculionidae)

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          Abstract

          Ceutorhynchus obstrictus (Marsham, 1802) is a serious pest of oilseed rape ( Brassica napus L.) in Europe and the USA. We have determined a 20,124 bp mitogenome of C. obstrictus which includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 2,773 bp. The base composition was AT-biased (81.4%). Hypothetical ORFs are identified in the control region. Phylogenetic trees present that C. oibstricus is clustered with Alcides juglans (Alcidinae). It also shows polyphyletic manner for two tribes, requiring more mitogenomes to resolve it.

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          Most cited references 15

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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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            The Sequence Alignment/Map format and SAMtools

            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

              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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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                19 September 2019
                2019
                : 4
                : 2
                : 3096-3098
                Affiliations
                [a ]Department of Plant Medicine, Gyeongsang National University , Jinju, Republic of Korea;
                [b ]InfoBoss Co., Ltd , Seolleung-ro, Seoul, Gangnam-gu, Republic of Korea;
                [c ]InfoBoss Research Center , Seolleung-ro, Seoul, Gangnam-gu, Republic of Korea;
                [d ]Department of Plant Medicine, Sunchon National University , Sunchon, Korea;
                [e ]Institute of Agriculture and Life Science, Gyeongsang National University , Jinju, Republic of Korea
                Author notes
                [*]

                Indicates co-first authors.

                CONTACT Jongsun Park starflr@ 123456infoboss.co.kr InfoBoss Co., Ltd , 301 room, 670, Seolleung-ro, Seoul, Gangnam-gu, Republic of Korea;
                Wonhoon Lee wonhoon@ 123456gnu.ac.kr Department of Plant Medicine, Gyeongsang National University , Jinju, 52828, Republic of Korea
                Article
                1667279
                10.1080/23802359.2019.1667279
                7706778
                © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                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.

                Page count
                Figures: 1, Tables: 0, Pages: 3, Words: 1433
                Product
                Categories
                Research Article
                Mitogenome Announcement

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