Chromosome-Level Genome Assembly and Annotation of a Sciaenid Fish,  Argyrosomus japonicus

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Abstract

Argyrosomus japonicus is an economically and ecologically important fish species in the family Sciaenidae with a wide distribution in the world’s oceans. Here, we report a high-quality, chromosome-level genome assembly of A. japonicus based on PacBio and Hi-C sequencing technology. A 673.7-Mb genome containing 282 contigs with an N50 length of 18.4 Mb was obtained based on PacBio long reads. These contigs were further ordered and clustered into 24 chromosome groups based on Hi-C data. In addition, a total of 217.2 Mb (32.24% of the assembled genome) of sequences were identified as repeat elements, and 23,730 protein-coding genes were predicted based on multiple approaches. More than 97% of BUSCO genes were identified in the A. japonicus genome. The high-quality genome assembled in this work not only provides a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of A. japonicus but also lays a solid foundation for the study of Sciaenidae evolution.

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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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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis (2014)

Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

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MUSCLE: multiple sequence alignment with high accuracy and high throughput.

R. C. Edgar (2004)

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

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Author and article information

Contributors

B T E Venkatesh: Role: Associate Editor

Journal

Journal ID (nlm-ta): Genome Biol Evol

Journal ID (iso-abbrev): Genome Biol Evol

Journal ID (publisher-id): gbe

Title: Genome Biology and Evolution

Publisher: Oxford University Press

ISSN (Electronic): 1759-6653

Publication date Collection: February 2021

Publication date (Electronic): 23 February 2021

Publication date PMC-release: 23 February 2021

Volume: 13

Issue: 2

Electronic Location Identifier: evaa246

Affiliations

[1 ] First Institute of Oceanography, Ministry of Natural Resources , Qingdao, Shandong, China

[2 ] Fishery College, Zhejiang Ocean University , Zhoushan, Zhejiang, China

[3 ] Wuhan Gooalgene Technology Co., Ltd. , Wuhan, Hubei, China

Author notes

Corresponding author: E-mail: gaotianxiang0611@ 123456163.com .

Article

Publisher ID: evaa246

DOI: 10.1093/gbe/evaa246

PMC ID: 7874996

PubMed ID: 33484557

SO-VID: 0772a364-21b9-4df4-866a-3a2b1215b54e

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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date accepted : 17 November 2020

Page count

Pages: 5

Funding

Funded by: National Natural Science Foundation of China, DOI 10.13039/501100001809;

Award ID: 41706187

Award ID: 41776171

Funded by: National Key R&D Program of China;

Award ID: 2019YFD0901301

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Chromosome-Level Genome Assembly and Annotation of a Sciaenid Fish, Argyrosomus japonicus

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Genome Integrity

Most cited references 30

Fast and accurate short read alignment with Burrows–Wheeler transform

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

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