解析单倍型的山葵（辣根）基因组染色体水平组装。

Haplotype-resolved chromosomal-level assembly of wasabi (Eutrema japonicum) genome.

机构信息

School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan.

Gifu University, Faculty of Applied Biological Sciences, 1-1 Yanagido, Gifu City, Gifu, 501-1193, Japan.

出版信息

Sci Data. 2023 Jul 11;10(1):441. doi: 10.1038/s41597-023-02356-z.

DOI:10.1038/s41597-023-02356-z

PMID:37433828

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10336049/

Abstract

In Japan, wasabi (Eutrema japonicum) is an important traditional condiment, and is recognized as an endemic species. In the present study, we generated a chromosome-level and haplotype-resolved reference genome for E. japonicum using PacBio CLR (continuous long reads), Illumina, and Hi-C sequencing data. The genome consists of 28 chromosomes that contain 1,512.1 Mb of sequence data, with a scaffold N50 length of 55.67 Mb. We also reported the subgenome and haplotype assignment of the 28 chromosomes by read-mapping and phylogenic analysis. Three validation methods (Benchmarking Universal Single-Copy Orthologs, Merqury, and Inspector) indicated that our obtained genome sequences were a high-quality and high-completeness genome assembly. Comparison of genome assemblies from previously published genomes showed that our obtained genome was of higher quality. Therefore, our genome will serve as a valuable genetic resource for both chemical ecology and evolution research of the genera Eutrema and Brassicaceae, as well as for wasabi breeding.

摘要

在日本，山葵（Eutrema japonicum）是一种重要的传统调味品，被认为是特有物种。在本研究中，我们使用 PacBio CLR（连续长读长）、Illumina 和 Hi-C 测序数据生成了 E. japonicum 的染色体水平和单倍型解析参考基因组。该基因组由 28 条染色体组成，包含 1,512.1 Mb 的序列数据，支架 N50 长度为 55.67 Mb。我们还通过读映射和系统发育分析报告了 28 条染色体的亚基因组和单倍型分配。三种验证方法（基准通用单拷贝直系同源物、Merqury 和 Inspector）表明，我们获得的基因组序列是高质量和高完整性的基因组组装。与先前发表的基因组的基因组组装比较表明，我们获得的基因组质量更高。因此，我们的基因组将成为 Eutrema 和十字花科属的化学生态学和进化研究以及山葵育种的宝贵遗传资源。