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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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.

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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): 19 September 2019

Publication date (Electronic, collection): 2019

Volume: 4

Issue: 2

Pages: 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

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[*]

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

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Jongsun Park https://orcid.org/0000-0003-0786-4701

Article

Publisher ID: 1667279

DOI: 10.1080/23802359.2019.1667279

PMC ID: 7706778

PubMed ID: 33365869

SO-VID: ab01e8db-7ef3-4664-8fb3-8c338214f28a

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.

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

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Coleoptera

Most cited references 15

Trimmomatic: a flexible trimmer for Illumina sequence data

The Sequence Alignment/Map format and SAMtools

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

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