Mixed-Mating Model of Reproduction Revealed in European Phytophthora cactorum by ddRADseq and Effector Gene Sequence Data

Abstract

A population study of Phytophthora cactorum was performed using ddRADseq sequence variation analysis completed by the analysis of effector genes—RXLR6, RXLR7 and SCR113. The population structure was described by F-statistics, heterozygosity, nucleotide diversity, number of private alleles, number of polymorphic sites, kinship coefficient and structure analysis. The population of P. cactorum in Europe seems to be structured into host-associated groups. The isolates from woody hosts are structured into four groups described previously, while isolates from strawberry form another group. The groups are diverse in effector gene composition and the frequency of outbreeding. When populations from strawberry were analysed, both asexual reproduction and occasional outbreeding confirmed by gene flow among distinct populations were detected. Therefore, distinct P. cactorum populations differ in the level of heterozygosity. The data support the theory of the mixed-mating model for P. cactorum, comprising frequent asexual behaviour and inbreeding alternating with occasional outbreeding. Because P. cactorum is not indigenous to Europe, such variability is probably caused by multiple introductions of different lineages from the area of its original distribution, and the different histories of sexual recombination and host adaptation of particular populations.

A Barcode-Based Phylogenetic Characterization of Phytophthora cactorum Identifies Two Cosmopolitan Lineages with Distinct Host Affinities and the First Report of Phytophthora pseudotsugae in California

“…Based on its placement and the comparison of the single-locus trees, the Chinese strain D-1, from Panax notoginseng , was determined to be P. ×serendipita and not P. cactorum , as originally designated in GenBank ( Figure 2 ). Our results do not support the hypothesis that P. hedraiandra and P. cactorum may be conspecific [ 25 , 26 ] unless the entire subclade is considered a single species.…”

“…Describing intraspecific diversity is difficult, and traditional phylogenetic methods are limited, even for a homothallic species such as P. cactorum that is predominantly asexual [ 26 ]. Although the four intraspecific lineages we identified clustered relatively consistently across our phylogenies and networks ( Figure 2 , Figure 3 , Figure 4 , Figure 5 , Figure 6 , Figure 7 , Figure 8 and Figure S5 ), the topology of the relationships between the lineages was not consistent.…”

“…It is not clear to what extent human activity is responsible for these putative hybrids. The intermediate placement of strain D-1 in the cox2+spacer only tree ( Figure S2 ) could also be interpreted as arising from incomplete lineage sorting rather than recent hybridization [ 26 , 67 , 68 , 69 ]. The Eurasian P. ×serendipita lineage, along with several P. cactorum isolates from Finland (isolated from Betula and water) were consistently inferred to be the most early-diverging within the species ( Figure 2 , Figure 4 and Figures S2 and S3 ).…”

“…Pánek et al (2016 & 2021) [ 25 , 26 ] found higher genetic diversity in European strains of P. ×serendipita than of P. cactorum , concluding that P. cactorum was not indigenous to Europe; Jung (2009) [ 27 ] found P. cactorum to have a largely urban distribution within Bavaria. Based on the inclusion of many isolates from New York state, Eikemo et al (2004) [ 20 ] suggested that the leather rot-associated, wider host-range lineage, may have originated in North America; Bhat et al (2006) [ 23 ] saw considerable intraspecific diversity within a collection of mostly agricultural isolates from California.…”

Use of metalaxyl against some soil plant pathogens of the class Peronosporomycetes - A review and two case studies

“…The results show that P. cactorum itself has high resistance variability, despite the fact that our case studies only comprise isolates of the genetic lineage "S", one of a total of five lineages discovered only recently (Pánek et al 2021a); its total level of resistance variability can thus be assumed to be even higher. This finding together with previous findings looks important, since they make the choice of the proper protection method for strawberries even more complicated.…”