Whole genome analysis of the koa wilt pathogen ( Fusarium oxysporum f. sp. koae ) and the development of molecular tools
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RESEARCH ARTICLE
Open Access
Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring John T. Dobbs1, Mee-Sook Kim2, Nicklos S. Dudley3, Ned B. Klopfenstein4, Aileen Yeh3, Robert D. Hauff5, Tyler C. Jones3, R. Kasten Dumroese4, Philip G. Cannon6 and Jane E. Stewart1*
Abstract Background: Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs. Results: This study presents whole genome analyses of one highly virulent Fo koae isolate and one nonpathogenic F. oxysporum (Fo) isolate. These analyses allowed for the identification of putative lineage-specific DNA and predicted genes necessary for disease development on koa. Using putative chromosomes and predicted gene comparisons, Fo koae-exclusive, virulence genes were identified. The putative lineage-specific DNA included identified genes encoding products secreted in xylem (e. g., SIX1 and SIX6) that may be necessary for disease development on koa. Unique genes from Fo koae were used to develop pathogen-specific PCR primers. These diagnostic primers allowed target amplification in the characterized highly virulent Fo koae isolates but did not allow product amplification in low-virulence or non-pathogenic isolates of Fo. Thus, primers developed in this study will be useful for early detection and monitoring of highly virulent strains of Fo koae. Isolate verification is also important for disease resistance-breeding programs that require a diverse set of highly virulent Fo koae isolates for their disease-screening assays to develop disease-resistant koa. Conclusions: These results provide the framework for understanding the pathogen genes necessary for koa wilt disease and the genetic variation of Fo koae populations across the Hawaiian Islands. Keywords: Fusarium oxysporum, Lineage-specific DNA, Virulence genes, PCR primer, Haplotypes, Acacia koa
* Correspondence: [email protected] 1 Colorado State University, Department of Agricultural Biology, 1177 Campus Delivery, Fort Collins, CO 80523, USA Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted
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