The complete genome assembly of Astragalus membranaceus: enabling more accurate genetic research.

IF 11.8 2区生物学 Q1 MULTIDISCIPLINARY SCIENCES

GigaScience Pub Date : 2025-01-06 DOI:10.1093/gigascience/giaf117

Huibin Qin, Aohui Li, Shuyu Zhong, Huazhi Wang, Hongling Tian

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引用次数: 0

Abstract

Background: Astragalus membranaceus (Fisch.) Bunge is a globally significant medicinal plant renowned for its potent immunomodulatory and antioxidant properties. However, the existing reference genome for this species remains incomplete, characterized by fragmented assemblies and the absence of centromeric and telomeric regions, thereby limiting comprehensive exploration of the genetic mechanisms underlying its key traits.

Findings: We hereby present the first complete genome assembly for A. membranaceus (Fisch.) Bge "AM-T2T," achieved through the integration of PacBio HiFi, ultra-long Oxford Nanopore Technologies, and Hi-C sequencing. The assembly achieved a total size of 1.39 Gb with an N50 of 180.45 Mb. The genome exhibits remarkable completeness (99.63% BUSCO completeness; long terminal repeat assembly index of 22.67) and high accuracy (quality value of 57.51; Genome Continuity Inspector score of 36.23). It features annotations of 64.22% repetitive sequences, 16 telomeres, 8 centromeres, 32,600 high-confident genes, 248 cytochrome P450 monooxygenases (CYP450s), and 163 uridine diphosphate glycosyltransferases. Notably, 158.58 Mb of previously unassembled regions were resolved, harboring 4 CYP450s. Additionally, 2,267 unique genes and 20,652 conserved genes were identified within the AM-T2T genome. Comparative analysis with Astragalus mongholicus assembly revealed 1,413 structural variations.

Conclusions: This complete genome assembly of A. membranaceus represents a significant advancement in the genomic characterization of A. membranaceus, providing a robust resource that will bolster genetic research, breeding programs, and medicinal applications.

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黄芪全基因组组装：实现更精确的基因研究。

背景：黄芪（黄芪属）邦吉是一种全球重要的药用植物，以其有效的免疫调节和抗氧化特性而闻名。然而，该物种现有的参考基因组仍然不完整，其特点是片段化组装，缺乏着丝粒和端粒区域，从而限制了对其关键性状遗传机制的全面探索。研究结果：本文首次报道了A. membrane aceus （Fisch.）的完整基因组组装。Bge“AM-T2T”，通过整合PacBio HiFi，超长牛津纳米孔技术和Hi-C测序实现。该基因组全长1.39 Gb， N50为180.45 Mb。该基因组具有显著的完整性（99.63% BUSCO完整性，长末端重复序列组装指数为22.67）和较高的准确性（质量值为57.51，genome Continuity Inspector评分为36.23）。它具有64.22%重复序列的注释，16个端粒，8个着丝粒，32,600个高自信基因，248个细胞色素P450单加氧酶（cyp450）和163个尿苷二磷酸糖基转移酶。值得注意的是，158.58 Mb先前未组装的区域被分解，包含4个cyp450。此外，在AM-T2T基因组中鉴定出2267个独特基因和20652个保守基因。与蒙古黄芪组合比较，发现1413个结构变异。结论：这一完整的膜拟南毛藻基因组组装代表了膜拟南毛藻基因组特征的重大进展，为支持遗传研究、育种计划和医学应用提供了强有力的资源。

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.