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九刺鱼(林奈,1758年)的基因组序列。

The genome sequence of the nine-spined stickleback, (Linnaeus, 1758).

作者信息

Hänfling Bernd, Smith Alan

机构信息

Institute for Biodiversity and Freshwater Conservation, University of Highlands and Islands, Inverness, Scotland, UK.

School of Natural Sciences, University of Hull, Hull, England, UK.

出版信息

Wellcome Open Res. 2023 Dec 5;8:555. doi: 10.12688/wellcomeopenres.20354.1. eCollection 2023.

DOI:10.12688/wellcomeopenres.20354.1
PMID:39114814
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11303943/
Abstract

We present a genome assembly from an individual male (the nine-spined stickleback; Chordata; Actinopteri; Gasterosteiformes; Gasterosteidae). The genome sequence is 480.4 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.57 kilobases in length.

摘要

我们展示了一个雄性个体(九刺鱼;脊索动物门;辐鳍鱼纲;刺鱼目;刺鱼科)的基因组组装结果。基因组序列跨度为480.4兆碱基。大部分组装序列被构建成21条染色体假分子。线粒体基因组也已组装完成,长度为16.57千碱基。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/2e5273b5bb3c/wellcomeopenres-8-22539-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/5ab998229464/wellcomeopenres-8-22539-g0000.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/dae0da17e7e5/wellcomeopenres-8-22539-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/23f931ff216d/wellcomeopenres-8-22539-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/23ecc71deb48/wellcomeopenres-8-22539-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/2e5273b5bb3c/wellcomeopenres-8-22539-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/5ab998229464/wellcomeopenres-8-22539-g0000.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/dae0da17e7e5/wellcomeopenres-8-22539-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/23f931ff216d/wellcomeopenres-8-22539-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/23ecc71deb48/wellcomeopenres-8-22539-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/327a/11303943/2e5273b5bb3c/wellcomeopenres-8-22539-g0004.jpg

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本文引用的文献

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G3 (Bethesda). 2024 Aug 7;14(8). doi: 10.1093/g3journal/jkae126.
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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.MitoHiFi:一个从 PacBio 高保真reads 组装线粒体基因组的 Python 分析流程
BMC Bioinformatics. 2023 Jul 18;24(1):288. doi: 10.1186/s12859-023-05385-y.
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YaHS: yet another Hi-C scaffolding tool.YaHS:另一个 Hi-C 支架工具。
Bioinformatics. 2023 Jan 1;39(1). doi: 10.1093/bioinformatics/btac808.
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BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.BUSCO 更新:用于真核生物、原核生物和病毒基因组评分的新颖且简化的工作流程以及更广泛和更深的系统发育覆盖范围。
Mol Biol Evol. 2021 Sep 27;38(10):4647-4654. doi: 10.1093/molbev/msab199.
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Automated improvement of stickleback reference genome assemblies with Lep-Anchor software.利用 Lep-Anchor 软件自动改进棘鱼参考基因组组装。
Mol Ecol Resour. 2021 Aug;21(6):2166-2176. doi: 10.1111/1755-0998.13404. Epub 2021 May 12.
6
Towards complete and error-free genome assemblies of all vertebrate species.致力于完成所有脊椎动物物种的完整且无错误的基因组组装。
Nature. 2021 Apr;592(7856):737-746. doi: 10.1038/s41586-021-03451-0. Epub 2021 Apr 28.
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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.使用带有 hifiasm 的相定装配图进行单体型解析从头组装。
Nat Methods. 2021 Feb;18(2):170-175. doi: 10.1038/s41592-020-01056-5. Epub 2021 Feb 1.
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Significantly improving the quality of genome assemblies through curation.通过编辑显著提高基因组组装的质量。
Gigascience. 2021 Jan 9;10(1). doi: 10.1093/gigascience/giaa153.
9
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.Merqury:基因组组装的无参考质量、完整性和相位评估。
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Mol Ecol. 2020 May;29(9):1642-1656. doi: 10.1111/mec.15435. Epub 2020 May 15.