Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4).

IF 11.8 2区生物学 Q1 MULTIDISCIPLINARY SCIENCES

GigaScience Pub Date : 2025-01-06 DOI:10.1093/gigascience/giaf001

Yan Wang, Xiaopeng Hao, Chunhai Chen, Haigang Wang, Peng Gao, Xukui Yang, Xue Dong, Huibin Qin, Meng Li, Sen Hou, Jianbo Jian, Jianwu Chang, Jing Wu, Zhixin Mu

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引用次数: 0

Abstract

Background: Common bean is a significant grain legume in human diets. However, the lack of a complete reference genome for common beans has hindered efforts to improve agronomic cultivars.

Findings: Herein, we present the first telomere-to-telomere (T2T) genome assembly of common bean (Phaseolus vulgaris L., YP4) using PacBio High-Fidelity reads, ONT ultra-long sequencing, and Hi-C technologies. The assembly resulted in a genome size of 560.30 Mb with an N50 of 55.11 Mb, exhibiting high completeness and accuracy (BUSCO score: 99.5%, quality value (QV): 54.86). The sequences were anchored into 11 chromosomes, with 20 of 22 telomeres identified, leading to the formation of 9 T2T pseudomolecules. Furthermore, we identified repetitive elements accounting for 61.20% of the genome and predicted 29,925 protein-coding genes. Phylogenetic analysis suggested an estimated divergence time of approximately 11.6 million years ago between P. vulgaris and Vigna angularis. Comparative genome analysis revealed the expanded gene families and variations between YP4 and G19833 associated with defense response.

Conclusions: The T2T reference genome and genomic insights presented here are crucial for future genetic studies not only in common bean but also in other legumes.

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豌豆（Phaseolus vulgaris L., YP4）的端粒-端粒基因组。

背景：普通豆是人类饮食中重要的谷物豆类。然而，缺乏完整的普通豆参考基因组阻碍了改良农艺品种的努力。研究结果：在此，我们利用PacBio高保真reads、ONT超长测序和Hi-C技术首次展示了普通豆（Phaseolus vulgaris L., YP4）的端粒到端粒（T2T）基因组组装。组装得到的基因组大小为560.30 Mb， N50为55.11 Mb，具有较高的完整性和准确性（BUSCO评分：99.5%，质量值（QV）： 54.86）。这些序列被固定在11条染色体上，22个端粒中有20个被确定，从而形成了9个T2T假分子。此外，我们发现重复元件占基因组的61.20%，并预测了29,925个蛋白质编码基因。系统发育分析表明，P. vulgaris和Vigna angularis的分化时间约为1160万年前。比较基因组分析揭示了YP4和G19833与防御反应相关的基因家族扩展和变异。结论：T2T参考基因组和本文提出的基因组见解对未来的遗传研究至关重要，不仅对普通豆，对其他豆类也是如此。

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

GigaScience MULTIDISCIPLINARY SCIENCES-

CiteScore

15.50

自引率

1.10%

发文量

119

审稿时长

1 weeks

期刊介绍： GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.