Evidence map›Paper›PMID 42801418›Full record

ArticleWorld journal of microbiology & biotechnology2026

Comparative-genomics-guided development of an isothermal assay for rapid detection of Fusarium oxysporum f. sp. phaseoli.

Kun Qian, Yuxin Zhang, Yang Chen, Simeng Chang, Guohua Chen, Jianlong Zhao, Zhenchuan Mao, Jian Ling, Yanlin Li

Abstract readComparative Study
PubMed Publisher
In one paragraph

Article in World journal of microbiology & biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

9 authors.

Kun QianState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Yuxin ZhangState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Yang ChenState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Simeng ChangState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Guohua ChenState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Jianlong ZhaoState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Zhenchuan MaoState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Jian LingState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. lingjian@caas.cn.
Yanlin LiCollege of Horticulture, Hunan Agricultural University, Changsha, 410128, China. liyanlin@hunau.edu.cn.

Funding

Agriculture Research System of China CARS-23National Key Research and Development Program of China 2024YFD1400100National Natural Science Foundation of China 31571962
6 · The paper itself

Abstract

Accurate identification of closely related lineages within the Fusarium oxysporum species complex remains challenging because commonly used DNA barcode regions often provide insufficient resolution at the forma specialis level. In this study, comparative genomics approach was combined with enzyme-mediated duplex exponential amplification (EmDEA) to develop a rapid molecular assay for F. oxysporum f. sp. phaseoli (FOP). A FOP strain LM-2 was characterized by morphological, molecular, and pathogenicity analyses. A chromosome-level genome assembly of the strain comprising 14 pseudochromosomes was generated using short-read, long-read, and Hi-C sequencing. Comparative analysis with seven other F. oxysporum genomes identified 1.004 Mb of candidate diagnostic regions. A 9.82-kb region on chromosome 11 was selected, and a 1,032-bp fragment designated TC4-2 was experimentally validated and used for primer and probe design. The resulting one-tube EmDEA assay was completed at 42 °C within 30 min. Positive amplification was obtained from three tested FOP isolates, whereas no effective amplification was observed in 12 tested non-target fungi. The conservative analytical detection limit was 40 pg µL⁻¹ purified genomic DNA. The assay also detected FOP DNA in purified DNA extracted from diseased cowpea stems and field soil. These results demonstrate a comparative-genomics-guided workflow for developing rapid closed-tube assays for closely related fungal pathogens.

Indexed as

FusariumGenomicsNucleic Acid Amplification TechniquesDNA, FungalDNA PrimersGenome, FungalPhylogenyPlant DiseasesSensitivity and SpecificityDNA, FungalDNA PrimersComparative genomicsDiagnostic targetEnzyme-mediated duplex exponential amplificationFungal pathogen detectionFusarium oxysporum f. sp. phaseoliIsothermal amplification

Identifiers

PMID42801418

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.