Comparative Genomics of Bremia lactucae

Bremia lactucae is a biotrophic oomycete responsible for lettuce downy mildew.  This disease is controlled by the use of resistant cultivars and fungicide applications; however, B. lactucae rapidly overcomes resistance genes and develops fungicide insensitivity. The reference genome of B. lactucae isolate SF5 has been sequenced using a combination of Illumina, Moleculo and PacBio technologies. Over 100 MB have been assembled revealing a highly heterozygous genome containing ~10,000 predicted gene models. We have sequenced an additional 47 isolates collected over the past 40 years from different geographical locations worldwide with different virulence phenotypes, some of which are near-isogenic somatic variants that differ in their ability to overcome individual resistance genes. These genomes have been mined for candidate effectors and other pathogenicity-related proteins using string searches, HMMs, and evidence of positive selection for diversity. The subset of effectors containing the conserved N-terminal RxLR motif for secretion is well represented in these genomes. Of those, the majority are present in many of the isolates; only a few are unique to a small number of isolates. The expression patterns of the predicted effectors and their genetic association with certain virulence phenotypes will be used to select candidates for functional validation. This study provides enabling data for more detailed population studies that will be used to inform the rational deployment of resistance genes.