中国青鳉染色体级别的高质量基因组组装。

A high-quality chromosome-level genome assembly of the Chinese medaka Oryzias sinensis.

机构信息

Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.

Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.

出版信息

Sci Data. 2024 Mar 28;11(1):322. doi: 10.1038/s41597-024-03173-8.

DOI:10.1038/s41597-024-03173-8

PMID:38548787

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10978949/

Abstract

Oryzias sinensis, also known as Chinese medaka or Chinese ricefish, is a commonly used animal model for aquatic environmental assessment in the wild as well as gene function validation or toxicology research in the lab. Here, a high-quality chromosome-level genome assembly of O. sinensis was generated using single-tube long fragment read (stLFR) reads, Nanopore long-reads, and Hi-C sequencing data. The genome is 796.58 Mb, and a total of 712.17 Mb of the assembled sequences were anchored to 23 pseudo-chromosomes. A final set of 22,461 genes were annotated, with 98.67% being functionally annotated. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of genome assembly and gene annotation reached 95.1% (93.3% single-copy) and 94.6% (91.7% single-copy), respectively. Furthermore, we also use ATAC-seq to uncover chromosome transposase-accessibility as well as related genome area function enrichment for Oryzias sinensis. This study offers a new improved foundation for future genomics research in Chinese medaka.

摘要

青鳉（Oryzias sinensis），又称日本青鳉或中国青鳉，是一种常用的水生环境评估动物模型，适用于野外以及实验室中的基因功能验证或毒理学研究。本研究利用单管长片段读长（stLFR）reads、纳米孔长读长和 Hi-C 测序数据，生成了青鳉的高质量染色体水平基因组组装。该基因组大小为 796.58 Mb，组装序列中总共 712.17 Mb 被锚定到 23 个假染色体上。最终注释了 22461 个基因，其中 98.67%具有功能注释。基因组组装和基因注释的基准通用单拷贝同源物（BUSCO）基准分别达到 95.1%（93.3%单拷贝）和 94.6%（91.7%单拷贝）。此外，我们还使用 ATAC-seq 来揭示青鳉的染色体转座酶可及性以及相关基因组区域功能富集情况。本研究为中国青鳉的未来基因组学研究提供了新的改进基础。