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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 non-pathogenic  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.    Supplementary information   Supplementary information  accompanies this paper at 10.1186/s12864-020-07156-y.

bmc genomics

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