Analysis of Whole-Genome for Alternaria Species Identification.

IF 4.2 2区 生物学 Q2 MICROBIOLOGY
Ying Yang, Yutong Gan, Wenjie Xu, Yuanhao Huang, Tianyi Xin, Rui Tan, Jingyuan Song
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引用次数: 0

Abstract

The genus Alternaria, functioning as a saprobe, endophyte, and plant pathogen, is widely distributed across various natural and human-impacted environments. Leaf spot and black spot diseases, caused by Alternaria species, are the most prevalent plant diseases within this genus, leading to significant reductions in crop yields and substantial economic losses. To facilitate the timely detection of Alternaria species during the early stages of infection, enable targeted treatments, and mitigate associated damages, we employed a species identification method based on Analysis of whole-GEnome (AGE). We downloaded 148 genomes, including 31 Alternaria species, from the NCBI GenBank database. Through bioinformatics analysis, we constructed a specific-target sequence library and selected a representative sequence per species. The specific target sequences of the seven exemplary Alternaria species were subsequently used for validation and rapid detection, utilizing Sanger sequencing and CRISPR-Cas12a technology, respectively. The results demonstrated that our method accurately identified the target species. Additionally, by combining Enzymatic Recombinase Amplification (ERA) with CRISPR-Cas12a, we achieved rapid and precise identification of genomic DNA samples, with a detection limit as low as 0.01 ng/µL within 30 min. Therefore, AGE proves to be a highly robust and efficient method for the detection of Alternaria species, offering broad potential for various applications.

互花孢属物种鉴定全基因组分析。
互花孢菌属广泛分布于各种自然和人为影响的环境中,是一种具有同源性、内生菌性和植物病原性的植物。由互花孢属植物引起的叶斑病和黑斑病是该属植物中最普遍的病害,导致作物产量大幅下降和重大经济损失。为了在感染早期及时发现Alternaria菌种,实现针对性治疗,减轻相关损害,我们采用了基于全基因组分析(AGE)的菌种鉴定方法。我们从NCBI GenBank数据库下载了148个基因组,其中包括31个Alternaria物种。通过生物信息学分析,构建了特定的靶序列文库,并为每个物种选择了具有代表性的序列。随后分别利用Sanger测序和CRISPR-Cas12a技术对7种典型Alternaria物种的特异性靶序列进行验证和快速检测。结果表明,该方法能准确地鉴定出目标物种。此外,我们将酶重组酶扩增(ERA)技术与CRISPR-Cas12a技术相结合,实现了基因组DNA样品的快速、精确鉴定,在30 min内的检出限低至0.01 ng/µL。因此,AGE被证明是一种高度稳健、高效的交替孢属(Alternaria)物种检测方法,具有广泛的应用潜力。
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
Journal of Fungi
Journal of Fungi Medicine-Microbiology (medical)
CiteScore
6.70
自引率
14.90%
发文量
1151
审稿时长
11 weeks
期刊介绍: Journal of Fungi (ISSN 2309-608X) is an international, peer-reviewed scientific open access journal that provides an advanced forum for studies related to pathogenic fungi, fungal biology, and all other aspects of fungal research. The journal publishes reviews, regular research papers, and communications in quarterly issues. Our aim is to encourage scientists to publish their experimental and theoretical results in as much detail as possible. Therefore, there is no restriction on paper length. Full experimental details must be provided so that the results can be reproduced.
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