Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring release_crv2xwjc5jhzzfjdch3dhmvq5m

Abstract

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> Development and application of DNA-based methods to distinguish highly virulent isolates of <jats:italic>Fusarium oxysporum</jats:italic> f. sp. <jats:italic>koae</jats:italic> [<jats:italic>Fo koae;</jats:italic> cause of koa wilt disease on <jats:italic>Acacia koa</jats:italic> (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs. </jats:sec> <jats:sec> <jats:title>Results</jats:title> This study presents whole genome analyses of one highly virulent <jats:italic>Fo koae</jats:italic> isolate and one non-pathogenic <jats:italic>F. oxysporum</jats:italic> (<jats:italic>Fo</jats:italic>) 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, <jats:italic>Fo koae</jats:italic>-exclusive, virulence genes were identified. The putative lineage-specific DNA included identified genes encoding products secreted in xylem (e. g., <jats:italic>SIX1</jats:italic> and <jats:italic>SIX6</jats:italic>) that may be necessary for disease development on koa. Unique genes from <jats:italic>Fo koae</jats:italic> were used to develop pathogen-specific PCR primers. These diagnostic primers allowed target amplification in the characterized highly virulent <jats:italic>Fo koae</jats:italic> isolates but did not allow product amplification in low-virulence or non-pathogenic isolates of <jats:italic>Fo</jats:italic>. Thus, primers developed in this study will be useful for early detection and monitoring of highly virulent strains of <jats:italic>Fo koae</jats:italic>. Isolate verification is also important for disease resistance-breeding programs that require a diverse set of highly virulent <jats:italic>Fo koae</jats:italic> isolates for their disease-screening assays to develop disease-resistant koa. </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> These results provide the framework for understanding the pathogen genes necessary for koa wilt disease and the genetic variation of <jats:italic>Fo koae</jats:italic> populations across the Hawaiian Islands. </jats:sec>
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