Mining the Uromyces transversalis genome for molecular markers and investigating genetic diversity of the quarintine-significant Gladiolus rust fungus

Abstract

Uromyces transversalis, the causal agent of Gladiolus rust, is quarantined in the EU and US because it can be devastating to Gladiolus spp. The aim of this research was to develop molecular markers to: (i) determine the origin of introductions of U. transversalis to the US, (ii) track the movement of genotypes, and (iii) understand the worldwide genetic diversity of the species. Whole genome sequencing was performed on three isolates collected in the US. Genomes were assembled de novo and searched for microsatellite regions. Primers were developed and tested on ten isolates from the US resulting in the identification of 24 robust polymorphic markers. Among 108 isolates collected, markers revealed polymorphism within each isolate with no diversity among isolates. The microsatellite loci and flanking regions showed high diversity and two divergent genomes within dikaryotic individuals, yet no diversity among individuals, suggesting that U. transversalis populations worldwide are strictly clonal. INDEX WORDS: Gladiolus rust; Uromyces transversalis; Whole Genome Sequencing; Microsatellites; Genetic Diversity; Clonal Population