东亚特有鱼类圆口铜鱼的染色体水平基因组组装

A chromosome-level genome assembly of East Asia endemic minnow Zacco platypus.

机构信息

State Key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.

Zhejiang Institute of Freshwater Fisheries, Huzhou, China.

出版信息

Sci Data. 2024 Mar 27;11(1):317. doi: 10.1038/s41597-024-03163-w.

DOI:10.1038/s41597-024-03163-w

PMID:38538602

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10973343/

Abstract

Zacco platypus is an endemic colorful freshwater minnow that is intensively distributed in East Asia. In this study, two adult female individuals collected from Haihe River basin were used for karyotypic study and genome sequencing, respectively. The karyotype formula of Z. platypus is 2N = 48 = 18 M + 24SM/ST + 6 T. We used PacBio long-read sequencing and Hi-C technology to assemble a chromosome-level genome of Z. platypus. As a result, an 814.87 Mb genome was assembled with the PacBio long reads. Subsequently, 98.64% assembled sequences were anchored into 24 chromosomes based on the Hi-C data. The chromosome-level assembly contained 54 scaffolds with a N50 length of 32.32 Mb. Repeat elements accounted for 52.35% in genome, and 24,779 protein-coding genes were predicted, with 92.11% were functionally annotated with the public databases. BUSCO analysis yielded a completeness score of 96.5%. This high-quality genome assembly provides valuable resources for future functional genomic research, comparative genomics, and evolutionary studies of genus Zacco.

摘要

圆口铜鱼是一种分布于东亚的特有彩色淡水小鱼。本研究分别从海河收集了两个成年雌性个体进行了核型研究和基因组测序。圆口铜鱼的核型公式为 2N=48=18M+24SM/ST+6T。我们使用 PacBio 长读测序和 Hi-C 技术组装了圆口铜鱼的染色体水平基因组。结果，使用 PacBio 长读序列组装出一个 814.87 Mb 的基因组。随后，根据 Hi-C 数据，98.64%的组装序列被锚定到 24 条染色体上。染色体水平的组装包含 54 个 scaffolds，N50 长度为 32.32 Mb。基因组中重复序列占 52.35%，预测到 24779 个蛋白质编码基因，其中 92.11%通过公共数据库进行了功能注释。BUSCO 分析得到了 96.5%的完整性得分。这个高质量的基因组组装为未来的功能基因组研究、比较基因组学和圆口铜鱼属的进化研究提供了有价值的资源。