Chromosome-level genome assembly of the Japanese sawyer beetle <i>Monochamus alternatus</i>

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Abstract

The Japanese sawyer beetle Monochamus alternatus (Coleoptera: Cerambycidae) is a pest in pine forests and acts as a vector for the pine wood nematode Bursaphelenchus xylophilus, which causes the pine wilt disease. We assembled a high-quality genome of M. alternatus at the chromosomal level using Illumina, Nanopore, and Hi-C sequencing technologies. The assembled genome is 767.12 Mb, with a scaffold N50 of 82.0 Mb. All contigs were assembled into ten pseudo-chromosomes. The genome contains 63.95% repeat sequences. We identify 16, 284 protein-coding genes in the genome, of which 11,244 were functionally annotated. The high-quality genome of M. alternatus provides an invaluable resource for the biological, ecological, and genetic study of this beetle and opens new avenues for understanding the transmission of pine wood nematode by insect vectors.

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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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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen, Yanqing Zhou, Yaru Chen … (2018)

Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.

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Author and article information

Contributors

Shi-Xiang Zong: zongshixiang@bjfu.edu.cn

Shu-Jun Wei:

ORCID: http://orcid.org/0000-0001-7398-0968

shujun268@163.com

Journal

Journal ID (nlm-ta): Sci Data

Journal ID (iso-abbrev): Sci Data

Title: Scientific Data

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2052-4463

Publication date (Electronic): 13 February 2024

Publication date PMC-release: 13 February 2024

Publication date Collection: 2024

Volume: 11

Electronic Location Identifier: 199

Affiliations

[1 ]Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, ( https://ror.org/04xv2pc41) Beijing, 100083 China

[2 ]GRID grid.418260.9, ISNI 0000 0004 0646 9053, Institute of Plant Protection, , Beijing Academy of Agriculture and Forestry Sciences, ; Beijing, 1000097 China

[3 ]Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, ( https://ror.org/0360dkv71) Beijing, 100091 China

Author information

Fang-Yuan Yang http://orcid.org/0000-0002-8435-3326

Shu-Jun Wei http://orcid.org/0000-0001-7398-0968

Article

Publisher ID: 3048

DOI: 10.1038/s41597-024-03048-y

PMC ID: 10864374

PubMed ID: 38351308

SO-VID: 09b20ea1-076b-4571-abff-031a7cf26c51

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 25 September 2023

Date accepted : 5 February 2024

Funding

Funded by: Program of Beijing Academy of Agriculture and Forestry Sciences (JKZX202208)

Funded by: National Key R&D Program of China (2021YFD1400900)

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Keywords: entomology,genome

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Keywords: entomology, genome

Chromosome-level genome assembly of the Japanese sawyer beetle Monochamus alternatus

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Coleoptera

Most cited references 40

Trimmomatic: a flexible trimmer for Illumina sequence data

Fast and accurate short read alignment with Burrows–Wheeler transform

fastp: an ultra-fast all-in-one FASTQ preprocessor

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