Microsatellite Profiling of Phytophthora ramorum

The population structure of P. ramorum NA1 was first reconstructed using microsatellite markers [34 (link),35 (link),36 (link)] and were compared to results from the SNP phylogeny. The 42 isolates were genotyped using six microsatellite loci (Table S2), PrMS39a, PrMS39b, PrMS45, PrM43a and PrMS43b [40 (link)] and locus 64 [41 (link)] using primers and thermal cycling conditions previously described [36 (link),40 (link),41 (link)]. Successful PCR amplifications were verified on 1.5% agarose gels and PCR products were subsequently sized on an ABI PRISM 3130xl sequencer (Applied Biosystems, Foster City, United States) using Rox 500 as size standard. Allele size assignments were performed using Genemarker (SoftGenetics LLC, State College, United States). Allelic data were formatted for the program GenAlex6 [42 (link)] which was used to identify identical MLGs among the 42 isolates. To illustrate the genetic variation among unique MLGs, a neighbor-joining tree was constructed based on Nei’s genetic distance, Da [43 (link)] using the program POPULATIONS 1.2.30 [44 ]. The tree was visualized using Nei’s genetic distance to identify points of reticulation. The microsatellite network was visualized on the program SplitsTree4 [45 (link)].