Analysis of Whole-Genome for <i>Alternaria</i> Species Identification
The genus <i>Alternaria</i>, 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 <i>Alternaria</i> species, are the most prevalent plant diseases wi...
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MDPI AG
2025-02-01
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| author | Ying Yang Yutong Gan Wenjie Xu Yuanhao Huang Tianyi Xin Rui Tan Jingyuan Song |
| author_facet | Ying Yang Yutong Gan Wenjie Xu Yuanhao Huang Tianyi Xin Rui Tan Jingyuan Song |
| author_sort | Ying Yang |
| collection | DOAJ |
| description | The genus <i>Alternaria</i>, 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 <i>Alternaria</i> 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 <i>Alternaria</i> 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 <i>Alternaria</i> 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 <i>Alternaria</i> 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 <i>Alternaria</i> species, offering broad potential for various applications. |
| format | Article |
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| language | English |
| publishDate | 2025-02-01 |
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| spelling | doaj-art-7c9e629e306d4e339b33506a589d87bb2025-08-20T01:48:46ZengMDPI AGJournal of Fungi2309-608X2025-02-0111318510.3390/jof11030185Analysis of Whole-Genome for <i>Alternaria</i> Species IdentificationYing Yang0Yutong Gan1Wenjie Xu2Yuanhao Huang3Tianyi Xin4Rui Tan5Jingyuan Song6School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, ChinaState Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaState Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaState Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaState Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaSchool of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, ChinaState Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaThe genus <i>Alternaria</i>, 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 <i>Alternaria</i> 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 <i>Alternaria</i> 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 <i>Alternaria</i> 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 <i>Alternaria</i> 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 <i>Alternaria</i> species, offering broad potential for various applications.https://www.mdpi.com/2309-608X/11/3/185Analysis of whole-GEnomebioinformatics analysis<i>Alternaria</i> species identificationSanger sequencingCRISPR-Cas12a |
| spellingShingle | Ying Yang Yutong Gan Wenjie Xu Yuanhao Huang Tianyi Xin Rui Tan Jingyuan Song Analysis of Whole-Genome for <i>Alternaria</i> Species Identification Journal of Fungi Analysis of whole-GEnome bioinformatics analysis <i>Alternaria</i> species identification Sanger sequencing CRISPR-Cas12a |
| title | Analysis of Whole-Genome for <i>Alternaria</i> Species Identification |
| title_full | Analysis of Whole-Genome for <i>Alternaria</i> Species Identification |
| title_fullStr | Analysis of Whole-Genome for <i>Alternaria</i> Species Identification |
| title_full_unstemmed | Analysis of Whole-Genome for <i>Alternaria</i> Species Identification |
| title_short | Analysis of Whole-Genome for <i>Alternaria</i> Species Identification |
| title_sort | analysis of whole genome for i alternaria i species identification |
| topic | Analysis of whole-GEnome bioinformatics analysis <i>Alternaria</i> species identification Sanger sequencing CRISPR-Cas12a |
| url | https://www.mdpi.com/2309-608X/11/3/185 |
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