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蓝宝石雀鲷的基因组：支持雀鲷科鱼类进化进一步研究的新资源。

The genome of the sapphire damselfish : a new resource to support further investigation of the evolution of Pomacentrids.

作者信息

Gairin Emma, Miura Saori, Takamiyagi Hiroki, Herrera Marcela, Laudet Vincent

机构信息

Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 904-0495, Onna-son, Okinawa, Japan.

Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10, Dah-Uen Rd, Jiau Shi, I-Lan 262, Taiwan.

出版信息

GigaByte. 2024 Dec 31;2024:gigabyte144. doi: 10.46471/gigabyte.144. eCollection 2024.

DOI:10.46471/gigabyte.144
PMID:39791000
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11711634/
Abstract

The number of high-quality genomes is rapidly increasing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus . Using PacBio long-read sequencing with 94.5× coverage, the genome of the Sapphire Devil, , was assembled and annotated. The final assembly comprises 896 Mb pairs across 91 contigs, with a BUSCO completeness of 97.6%, and 28,173 genes. Comparative analyses with chromosome-scale assemblies of related species identified contig-chromosome correspondences. This genome will be useful as a comparison to study specific adaptations linked to the symbiotic life of closely related anemonefish. Furthermore, is found in most tropical coastal areas of the Indo-West Pacific and could become a model for environmental monitoring. This work will expand coral reef research efforts, highlighting the power of long-read assemblies to retrieve high quality genomes.

摘要

跨分类群的高质量基因组数量正在迅速增加。然而，雀鲷科珊瑚礁鱼类的高质量基因组数量仍然有限，大多数研究集中在海葵鱼上。在这里，我们展示了雀鲷属鱼类的首个基因组组装。利用PacBio长读长测序技术，测序深度达94.5倍，对蓝魔雀鲷（Chrysiptera cyanea）的基因组进行了组装和注释。最终组装结果包含91个重叠群，共896 Mb对，BUSCO完整性为97.6%，含有28173个基因。与相关物种的染色体水平组装进行比较分析，确定了重叠群与染色体的对应关系。该基因组将有助于研究与近亲海葵鱼共生生活相关的特定适应性。此外，蓝魔雀鲷分布于印度-西太平洋的大多数热带沿海地区，有望成为环境监测的模型。这项工作将扩大珊瑚礁研究的范围，凸显长读长组装技术在获取高质量基因组方面的强大作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/6ed99b82d659/gigabyte-2024-144-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/32ffdae57e8b/gigabyte-2024-144-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/92dcab38591b/gigabyte-2024-144-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/03aea49cb052/gigabyte-2024-144-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/e2acd74b4bcc/gigabyte-2024-144-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/6ed99b82d659/gigabyte-2024-144-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/32ffdae57e8b/gigabyte-2024-144-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/92dcab38591b/gigabyte-2024-144-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/03aea49cb052/gigabyte-2024-144-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/e2acd74b4bcc/gigabyte-2024-144-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa22/11711634/6ed99b82d659/gigabyte-2024-144-g005.jpg

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本文引用的文献

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Anemonefishes: A model system for evolutionary genomics.海葵鱼：进化基因组学的模式系统。
F1000Res. 2023 Oct 27;12:204. doi: 10.12688/f1000research.130752.2. eCollection 2023.
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Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus.三斑原海豚基因组图谱。
G3 (Bethesda). 2023 Apr 11;13(4). doi: 10.1093/g3journal/jkac339.
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The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish.黄尾小丑鱼（Amphiprion clarkii）染色体水平基因组组装为研究海葵鱼的黑色素沉着提供了线索。
G3 (Bethesda). 2023 Mar 9;13(3). doi: 10.1093/g3journal/jkad002.
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A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris.假小丑鱼 Amphiprion ocellaris 的染色体级基因组组装。
G3 (Bethesda). 2022 May 6;12(5). doi: 10.1093/g3journal/jkac074.
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Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology.雀鲷科鱼类（Pomacentridae）的系统发育及体型和摄食生态的非对称多样化模式。
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Twelve years of SAMtools and BCFtools.SAMtools 和 BCFtools 十二年。
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BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.BRAKER2：借助蛋白质数据库，由GeneMark-EP+和AUGUSTUS支持的真核生物基因组自动注释工具。
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