Limited genetic diversity across pathogen populations responsible for the global emergence of boxwood blight identified using SSRs

Abstract

Boxwood blight is an emerging disease of ornamental as well as native boxwood. The disease became widely established in Europe at the beginning of the 21st century, prior to its more recent discovery in North America and Asia. Two sister‐species of fungi cause the disease, Calonectria pseudonaviculata (Cps) and C. henricotiae (Che). Prior efforts to quantify intraspecific genetic polymorphisms of Cps and Che have yielded little information, limiting the ability to understand the evolution and migration of these pathogens. This study describes the development and implementation of simple sequence repeat (SSR) markers to analyse genetic diversity from a global collection of Cps and Che isolates, representing major blight outbreaks since the disease was first identified in the UK in the late 1990s. Analysis of the Cps CB002 genome sequence identified 180 single copy SSR loci using stringent search criteria, 11 of which were polymorphic and used to screen a global sample of 306 isolates. Fourteen multilocus genotypes of Cps and two multilocus genotypes of Che were identified. Twelve of the 14 Cps genotypes differed from each other by a single allele. The most common Cps genotype was found on all continents where boxwood blight is confirmed. Based on measurement of linkage disequilibrium, Cps showed no evidence of sexual recombination. Further in silico analysis identified 1594 SSRs using relaxed SSR definition criteria. Comparison of these SSR‐containing loci with Cps and Che genome sequences representing three different genotypes demonstrated that single nucleotide polymorphisms might serve as informative genetic markers for future studies.

Mating genes in Calonectria and evidence for a heterothallic ancestral state

“…All additional available genome sequences for Calonectria spp. published to date ( Malapi-Wight et al 2016a , b , 2019 , Ye et al 2017 , LeBlanc et al 2019 ) were also screened for inclusion in this study of the mating type locus. These included three genome sequences of Ca.…”

Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata

“…However, in 2005, a second species— Che was identified from diseased boxwood in the UK and continental Europe [ 24 ]. Several studies have shown limited genetic diversity from natural populations of Che and Cps , consistent with the hypothesis of predominant asexual reproduction and introduced clonal lineages [ 8 , 37 , 38 ]. Malapi-Wight et al (2019) determined that populations of Cps have a single mating type idiomorph (MAT1-1) compared to populations of Che which possess the MAT1-2 idiomorph [ 44 ].…”

“…Malapi-Wight et al (2019) determined that populations of Cps have a single mating type idiomorph (MAT1-1) compared to populations of Che which possess the MAT1-2 idiomorph [ 44 ]. Separate studies demonstrated that pathogen populations have low genetic diversity and no evidence of sexual recombination, suggesting limited opportunities for mating with predominately clonal asexual reproduction [ 8 , 37 ]. Despite possessing opposite mating types and a sympatric geographic distribution in Europe and the UK, successful mating between Che and Cps has not been observed in nature or under laboratory conditions [ 7 , 37 , 44 ].…”

Boxwood Blight Disease: A Diagnostic Guide

“…In contrast to the widespread global distribution of Cps, Che is presently detected only in six European countries: Belgium, the Czech Republic, Germany, the Netherlands, Slovenia, and the United Kingdom (Bartíková et al 2020a(Bartíková et al , 2020bLeBlanc et al 2019) (Fig. 7).…”

“…Because the LAMP assays are based on isothermal DNA amplification, they do not require the use of thermal cyclers. Whole-genome sequences have also been used to confirm the identity of Cps isolates (Malapi-Wight et al 2016b), and several genome sequences are publicly available for both Che and Cps for comparative use (Crouch et al 2017;LeBlanc et al 2019).…”