裂唇鱼的染色体水平基因组组装

Chromosome-level genome assembly of the doctor fish (Garra rufa).

作者信息

Kon Tetsuo, Kon-Nanjo Koto, Handayani Kiki Syaputri, Zang Liqing, Fahrurrozi Fahrurrozi, Simakov Oleg, Gultom Victor David Nico, Shimada Yasuhito

机构信息

Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, 1030, Austria.

Research Center for Marine and Land Bioindustry, Research Organization for Earth Sciences and Maritime, BRIN. Jl. Raya Senggigi, Teluk Kodek, 83352, Indonesia.

出版信息

Sci Data. 2025 May 9;12(1):765. doi: 10.1038/s41597-025-05101-w.

DOI:10.1038/s41597-025-05101-w

PMID:40346083

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12064734/

Abstract

Garra rufa, or doctor fish, is a small cyprinid known for its high-temperature tolerance and its use in ichthyotherapy. Recently, this trait has gained interest as a model for human diseases, including infections and cancer xenografts, though limited genomic resources hinder experimental use. In this study, we have generated a high-quality, chromosome-level genome assembly of G. rufa using PacBio HiFi long-read sequencing and Hi-C technology. The genome is 1.38 Gb in size, with 25 chromosomes and a scaffold N50 of 49.3 Mb. Approximately 59% of the genome consists of repetitive elements, while 27,352 protein-coding genes were annotated, with 98.3% being functionally characterized. BUSCO analysis revealed 94.5% and 94.7% completeness for the genome assembly and annotated protein sequences, respectively. Notably, we identified two heat shock transcription factor (HSF) genes, 239 heat shock protein (HSP)-related genes, and 1,036 heat shock elements (HSEs) in regulatory regions. Phylogenetic analysis supports the placement of G. rufa within the Labeoninae subfamily. This genome assembly provides a valuable resource for advancing G. rufa as a model organism.

摘要

红腹锦鳚，或称“医生鱼”，是一种小型鲤科鱼类，以其耐高温能力及在鱼疗中的应用而闻名。近来，这一特性作为人类疾病（包括感染和癌症异种移植）的模型引起了关注，不过有限的基因组资源阻碍了其实验应用。在本研究中，我们利用PacBio HiFi长读长测序和Hi-C技术，生成了高质量的、染色体水平的红腹锦鳚基因组组装。该基因组大小为1.38Gb，有25条染色体，支架N50为49.3Mb。约59%的基因组由重复元件组成，同时注释了27352个蛋白质编码基因，其中98.3%具有功能特征。BUSCO分析显示，基因组组装和注释的蛋白质序列的完整性分别为94.5%和94.7%。值得注意的是，我们在调控区域鉴定出两个热休克转录因子（HSF）基因、239个热休克蛋白（HSP）相关基因和1036个热休克元件（HSE）。系统发育分析支持红腹锦鳚在野鲮亚科中的分类地位。这种基因组组装为将红腹锦鳚发展成为模式生物提供了宝贵资源。