Chromosome-level assembly and gene annotation of <i>Decapterus maruadsi</i> genome using Nanopore and Hi-C technologies

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Abstract

Decapterus maruadsi is one of the representative offshore fish in the Western Pacific. Since the last century, it has become a commercially valuable marine fishery species in the Western Pacific region. Despite its high economic value, there is still a lack of high-quality reference genome of D. maruadsi in germplasm resource evaluation research. Here we report a chromosome-level reference genome of D. maruadsi based on Nanopore sequencing and Hi-C technologies. The whole genome was assembled through 169 contigs with a total length of 723.69 Mb and a contig N50 length of 24.67 Mb. By chromosome scaffolding, 23 chromosomes with a total length of 713.58 Mb were constructed. In addition, a total of 199.49 Mb repetitive elements, 33,515 protein-coding genes, and 6,431 ncRNAs were annotated in the reference genome. This reference genome of D. maruadsi will provide a solid theoretical basis not only for the subsequent development of genomic resources of D. maruadsi but also for the formulation of policies related to the protection of D. maruadsi.

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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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Minimap2: pairwise alignment for nucleotide sequences

Heng Li (2018)

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.

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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Daehwan Kim, Joseph M Paggi, Chanhee Park … (2021)

Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT2, for representing and searching an expanded model of the human reference genome, in which a large catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate two initial applications of HISAT2: HLA typing, a critical need in human organ transplantation, and DNA fingerprinting, widely used in forensics. These applications are part of HISAT-genotype, with performance not only surpassing earlier computational methods, but matching or exceeding the accuracy of laboratory-based assays.

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Author and article information

Contributors

Peng Xu:

ORCID: http://orcid.org/0000-0002-1531-5078

xupeng77@xmu.edu.cn

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 January 2024

Publication date PMC-release: 13 January 2024

Publication date Collection: 2024

Volume: 11

Electronic Location Identifier: 69

Affiliations

[1 ]State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, ( https://ror.org/00mcjh785) Xiamen, 361102 China

[2 ]Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, ( https://ror.org/00mcjh785) Xiamen, 361102 China

Author information

Longyu Chen http://orcid.org/0000-0002-6149-1865

Zhixiong Zhou http://orcid.org/0000-0001-8283-4882

Fei Pu http://orcid.org/0000-0002-7472-7638

Tao Zhou http://orcid.org/0000-0002-2353-7404

Peng Xu http://orcid.org/0000-0002-1531-5078

Article

Publisher ID: 2912

DOI: 10.1038/s41597-024-02912-1

PMC ID: 10787795

PubMed ID: 38218740

SO-VID: 570136e2-b85d-4809-9e7e-da180fa8049b

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 : 19 April 2023

Date accepted : 2 January 2024

Funding

Funded by: Fundamental Research Funds for the Central Universities (No.20720200119)

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Keywords: genome,genomics

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Keywords: genome, genomics

Chromosome-level assembly and gene annotation of Decapterus maruadsi genome using Nanopore and Hi-C technologies

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Most cited references 45

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

Minimap2: pairwise alignment for nucleotide sequences

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

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