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Botrytis cinerea  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.  B. cinerea  is closely related to  Botrytis pseudocinerea , another broad host range species which often occurs in sympatry with  B. cinerea , and to several host-specific species including  Botrytis fabae  and  Botrytis calthae .  B. cinerea  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  B. cinerea ,  B. fabae , and  B. pseudocinerea . 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  B. cinerea  strains formed an as yet unknown population, referred to as group B, which was well separated from all other  B. cinerea  strains. Furthermore, the gene cluster for biosynthesis of the phytotoxin botcinic acid was missing in  B. cinerea  B strains.  B. cinerea  strains from the monocot  Iris pseudacorus  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  B. cinerea . Remarkably, these strains were much more aggressive on  Iris  than other  B. cinerea  strains, which is the first unequivocal example for host specialization in  B. cinerea . Our data reveal new insights into the genetic diversity of  B. cinerea  and provide evidence for intraspecific differentiation and different degrees of host adaptation of this polyphagous necrotrophic pathogen.

frontiers in plant science

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