The complete mitochondrial genome of <i>Aclees taiwanensis</i> Kôno, 1933 (Coleoptera: Curculionidae)

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Abstract

We sequenced the complete mitochondrial genome of Aclees taiwanensis collected in Korea. The circular mitogenome of A. taiwanensis is 17,435 bp, longer than that of Aclees cribratus, and includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a control region/D-loop. The AT ratio is 75.4%. Maximum-likelihood and Bayesian inference phylogenetic trees showed that A. taiwanensis was clustered with A. cribratus with full-support values for both trees.

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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): 10 August 2022

Publication date (Electronic, collection): 2022

Publication date PMC-release: 10 August 2022

Volume: 7

Issue: 8

Pages: 1460-1462

Affiliations

[a ]Department of Plant Medicine, Sunchon National University , Suncheon, 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 Research Center , Seoul, Republic of Korea

Wonhoon Lee wonhoon@ 123456gnu.ac.kr Institute of Agriculture and Life Science, Gyeongsang National University , Jinju, Republic of Korea

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

Article

Publisher ID: 2107440

DOI: 10.1080/23802359.2022.2107440

PMC ID: 9377266

SO-VID: b2ce95a4-b6c7-4860-8ee5-023f1ee411b0

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 Aclees taiwanensis Kôno, 1933 (Coleoptera: Curculionidae)

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Abstract

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Coleoptera

Most cited references 30

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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