Genetic Diversity of Botrytis cinerea Revealed by Multilocus Sequencing, and Identification of B. cinerea Populations Showing Genetic Isolation and Distinct Host Adaptation

Abstract

<i>Botrytis cinerea</i> is a world-wide occurring plant pathogen, causing pre- and post-harvest gray mold rot on a large number of fruit, vegetable, and flower crops. <i>B. cinerea</i> is closely related to <i>Botrytis pseudocinerea</i>, another broad host range species which often occurs in sympatry with <i>B. cinerea</i>, and to several host-specific species including <i>Botrytis fabae</i> and <i>Botrytis calthae</i>. <i>B. cinerea</i> populations have been shown to be genetically heterogeneous, and attempts have been made to correlate genetic markers to virulence and host adaptation. Here, we present the development of a multilocus sequence typing (MLST) scheme, with 10 genes selected for high variability and phylogenetic congruence, to evaluate the genetic diversity of <i>B. cinerea</i>, <i>B. fabae</i>, and <i>B. pseudocinerea</i>. Using PacBio-assisted simultaneous mass sequencing of PCR products, MLST analysis of about 100 strains from diverse geographical origins and years of isolation was performed, which resulted in high-resolution strain differentiation and robust species separation. Several <i>B. cinerea</i> strains formed an as yet unknown population, referred to as group B, which was well separated from all other <i>B. cinerea</i> strains. Furthermore, the gene cluster for biosynthesis of the phytotoxin botcinic acid was missing in <i>B. cinerea</i> B strains. <i>B. cinerea</i> strains from the monocot <i>Iris pseudacorus</i> were found to form a genetically distinct population, and contained an intact gene cluster for production of the red pigment bikaverin, which is usually degenerated in <i>B. cinerea</i>. Remarkably, these strains were much more aggressive on <i>Iris</i> than other <i>B. cinerea</i> strains, which is the first unequivocal example for host specialization in <i>B. cinerea</i>. Our data reveal new insights into the genetic diversity of <i>B. cinerea</i> and provide evidence for intraspecific differentiation and different degrees of host adaptation of this polyphagous necrotrophic pathogen.