红鲷（Rhomboplites aurorubens）的染色体水平基因组组装

Chromosome-level genome assembly of the Vermilion Snapper (Rhomboplites aurorubens).

作者信息

Roa-Varón A, Moulos P, Harter S, David A, Quattrini A M, Herrera S

机构信息

Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.

Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center, Alexander Fleming, Fleming 34, 16672, Vari, Greece.

出版信息

Sci Data. 2025 Jul 23;12(1):1281. doi: 10.1038/s41597-025-05573-w.

DOI:10.1038/s41597-025-05573-w

PMID:40701987

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12287329/

Abstract

Vermilion Snapper (Rhomboplites aurorubens, Lutjanidae) inhabits deep waters (20-300 m) from North America to Brazil and supports significant commercial and recreational fisheries. Despite its economic importance, the understanding of its basic biology remains limited. Classified as Vulnerable on the Red List due to overfishing, populations have declined by over 30% in recent generations. We assembled and annotated the first chromosome-scale genome of this species by combining PacBio long reads, Illumina short reads, and Hi-C data. The resulting assembly is 987.5 Mbp, with a scaffold N50 size of 41.3 Mbp, and includes 135 contigs clustered and ordered onto 24 chromosomes with 34,496 predicted genes. The high-quality assembly and annotation contained about 98% complete and single-copy BUSCO genes. It is the most complete, chromosome-level genome assembly of an Atlantic snapper to date. The genome assembly and supporting data are valuable tools for ecological and comparative genomics studies of snappers and other valuable commercial species within the family.

摘要

朱红笛鲷（Rhomboplites aurorubens，笛鲷科）栖息于从北美到巴西的深水区域（20 - 300米），是重要的商业和休闲渔业资源。尽管其具有经济重要性，但对其基本生物学的了解仍然有限。由于过度捕捞，该物种在《濒危物种红色名录》中被列为易危物种，其种群数量在近代下降了超过30%。我们通过结合PacBio长读长、Illumina短读长和Hi-C数据，组装并注释了该物种的首个染色体水平的基因组。最终的组装结果为987.5 Mbp，支架N50大小为41.3 Mbp，包括135个重叠群，这些重叠群被聚类并排列到24条染色体上，预测基因有34,496个。高质量的组装和注释包含约98%完整且单拷贝的BUSCO基因。这是迄今为止大西洋笛鲷最完整的染色体水平基因组组装。该基因组组装及相关支持数据是笛鲷及该科其他有价值商业物种的生态和比较基因组学研究的宝贵工具。