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

被引：5

作者：

Tanaka, Hiroyuki ^{[1
]}

Hori, Tatsuki ^{[1
]}

Yamamoto, Shohei ^{[2
]}

Toyoda, Atsushi ^{[3
]}

Yano, Kentaro ^{[4
]}

Yamane, Kyoko ^{[2
]}

Itoh, Takehiko ^{[1
]}

机构：

[1] Tokyo Inst Technol, Sch Life Sci & Technol, Meguro-ku, Tokyo 1528550, Japan

[2] Gifu Univ, Fac Appl Biol Sci, 1-1 Yanagido, Gifu, Gifu 5011193, Japan

[3] Natl Inst Genet, Comparat Genom Lab, Mishima, Shizuoka 4118540, Japan

[4] Tokyo Metropolitan Univ, Dept Biol Sci, Tokyo 1920397, Japan

来源：

SCIENTIFIC DATA | 2023年 / 10卷 / 01期

关键词：

PHYLOGENETIC ANALYSIS; PROVIDES; SYSTEM; MAFFT;

D O I：

10.1038/s41597-023-02356-z

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：12

共 39 条

[1]

[Anonymous], 2018, NCBI GenBank

[2]

[Anonymous], 2021, NCBI GenBank

[3] Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads [J].