大豆品种中黄13号的端粒到端粒基因组组装

IF 6 1区 农林科学 Q1 AGRONOMY
Anqi Zhang, Tangchao Kong, Baiquan Sun, Shizheng Qiu, Jiahe Guo, Shuyong Ruan, Yu Guo, Jirui Guo, Zhishuai Zhang, Yue Liu, Zheng Hu, Tao Jiang, Yadong Liu, Shuqi Cao, Shi Sun, Tingting Wu, Huilong Hong, Bingjun Jiang, Maoxiang Yang, Xiangyu Yao, Yang Hu, Bo Liu, Tianfu Han, Yadong Wang
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引用次数: 0

摘要

大豆(Glycine max)是全球重要的农业作物,其基因组的全面组装对于揭示其生物学特性和进化历史具有至关重要的意义。然而,先前的大豆基因组组装存在空白和不完整,这限制了对大豆的深入研究。在这里,我们利用PacBio Hifi和ONT超长读取技术,展示了中国大豆品种中黄13 (ZH13)基因组的端粒到端粒(T2T)组装。我们采用了多装配方法,集成了Hifiasm、NextDenovo和Canu,以最大限度地减少偏差并提高装配精度。该组合全长1,015,024,879 bp,有效地解决了之前困扰参考基因组的所有393个缺口。我们的注释工作确定了50,564个高置信度的蛋白质编码基因,其中707个是新的。与早期组合相比,ZH13-T2T显示出更长的染色体,421个不对齐区域(NARs), 112个结构变异(SVs)和大量重复元件的扩展。具体来说,我们鉴定出25.67 Mb的串联重复序列,富集5S和48S rnas,并表征了它们的基因型多样性。综上所述,我们获得了第一个完整的中国大豆品种T2T基因组。全面的注释,以及精确的着丝粒和端粒表征,以及对结构变异的见解,进一步增强了我们对大豆遗传和进化的理解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max
Soybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar Zhonghuang 13 (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution.
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来源期刊
Crop Journal
Crop Journal Agricultural and Biological Sciences-Agronomy and Crop Science
CiteScore
9.90
自引率
3.00%
发文量
638
审稿时长
41 days
期刊介绍: The major aims of The Crop Journal are to report recent progresses in crop sciences including crop genetics, breeding, agronomy, crop physiology, germplasm resources, grain chemistry, grain storage and processing, crop management practices, crop biotechnology, and biomathematics. The regular columns of the journal are Original Research Articles, Reviews, and Research Notes. The strict peer-review procedure will guarantee the academic level and raise the reputation of the journal. The readership of the journal is for crop science researchers, students of agricultural colleges and universities, and persons with similar academic levels.
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