Intra- and intergenomic variation of ploidy and clonality characterize Phytophthora capsici on Capsicum sp. in Taiwan​​
D. Barchenger, K. H. Lamour, Z. M., Sheu,, and S. Shrestha et al..  2017.  Mycological Progress.

Abstract:
Phytophthora capsici is a devastating disease ofpepper (Capsicum sp.) in Taiwan causing complete loss ofcommercial fields. The objective of this study was to charac-terize genetic diversity for 38 newly collected isolates andthree historical isolates. Analysis of data includes whole ge-nome sequence for two new isolates and for two isolates col-lected previously in 1987 and 1995. In addition, 63 singlenucleotide polymorphism loci were genotyped usingtargeted-sequencing, revealing 27 unique genotypes.Genotypes fell into three genetic groups: two of the groupscontain 90% (n = 33) of the 2016 isolates, are triploid (orhigher), are exclusively the A2 mating type and appear to betwo disti nct clonal lineages. The isolates from 2016 thatgrouped with the historical isolates are diploid and the A1mating type. Whole genome sequence revealed that ploidyvaries by linkage group, and it appears the A2 clonal lineagesmay have switched mating type due to increased ploidy. Mostof the isolates were recently race-typed on a set of differentialC. annuum, and a lthough there was no direct correlationbetween virulence and ploidy, many of the triploid isolateswere less virulent as compared to the historical diploid iso-l ates. The im plication s for breeding resistant p epper andconducting population analyses are discussed.