Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2.

IF 2.9 2区生物学 Q1 GENETICS & HEREDITY

DNA Research Pub Date : 2025-07-04 DOI:10.1093/dnares/dsaf016

Tsuyoshi Tanaka, Yuhi Haraguchi, Takatomo Todoroki, Daisuke Saisho, Tomomi Abiko, Hiroomi Kai

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引用次数: 0

Abstract

Current advances in next-generation sequencing (NGS) technology and assembling programs permit construct chromosome-level genome assemblies in various plants. In contrast to resequencing, the genome sequences provide comprehensive annotation data useful for plant genetics and breeding. Herein, we constructed a reference-based genome assembly of winter barley (H. vulgare ssp. vulgare) cv. 'Hayakiso 2' using long and short read NGS data and barley reference genome sequences from 'Morex'. We constructed 'Hayakiso 2' genome sequences covering 4.3 Gbp with 55,477 genes. Comparative genomics revealed that 14,106 genes had orthologs to two barley data, wheat (A, B, and D homoeologs, respectively), and rice. From the gene ontology analysis, 2,494 orthologs against wheat and rice but not two barley contained agricultural important genes, such as 'response to biotic and abiotic stress' and 'metabolic process'. Phylogenetic analysis using 76 pangenome data indicated that 'Hayakiso 2' was clustered into Japanese-type genomes with unique alleles. 'Hayakiso 2' genome sequences showed known genes related to flowering and facilitated barley breeding through the development of various markers related to agronomically important alleles such as tolerance to various types of biotic and abiotic stress. Therefore, 'Hayakiso 2' genome sequences will be used for the further barley breeding.

查看原文本刊更多论文

基于参考的日本大麦（Hordeum vulgare ssp）染色体规模组装。Hayakiso的变种；

当前新一代测序技术和组装程序的进展使得在各种植物中构建染色体水平的基因组组装成为可能。与重测序相比，基因组序列提供了对植物遗传和育种有用的全面注释数据。本文构建了冬大麦（H. vulgare ssp）基因组参考序列。)简历。“Hayakiso 2”使用了来自“Morex”的长、短读取NGS数据和大麦参考基因组序列。构建了Hayakiso 2号基因组序列，共包含55,477个基因，覆盖4.3 Gbp。比较基因组学显示，14106个基因与大麦、小麦（分别为A、B和D）和水稻具有同源性。从氧化石墨烯分析来看，小麦和水稻的2494个同源基因含有重要的农业基因，如“对生物和非生物胁迫的反应”和“代谢过程”。对76份泛基因组数据的系统发育分析表明，“隼草2号”具有独特的等位基因，属于日本型基因组。“Hayakiso 2”基因组序列显示了与开花相关的已知基因，并通过开发与农学上重要等位基因相关的各种标记促进了大麦育种，如对各种类型的生物和非生物胁迫的耐受性。因此，“隼草2号”基因组序列将用于进一步的大麦育种。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

DNA Research 生物-遗传学

CiteScore

6.00

自引率

4.90%

发文量

审稿时长

4.5 months

期刊介绍： DNA Research is an internationally peer-reviewed journal which aims at publishing papers of highest quality in broad aspects of DNA and genome-related research. Emphasis will be made on the following subjects: 1) Sequencing and characterization of genomes/important genomic regions, 2) Comprehensive analysis of the functions of genes, gene families and genomes, 3) Techniques and equipments useful for structural and functional analysis of genes, gene families and genomes, 4) Computer algorithms and/or their applications relevant to structural and functional analysis of genes and genomes. The journal also welcomes novel findings in other scientific disciplines related to genomes.