Multilocus Sequence Analysis of Selected Housekeeping- and Pathogenicity-Related Genes in Venturia inaequalis.

Monika Michalecka,Joanna Puławska

doi:10.3390/pathogens10040447

Abstract

The relationship between housekeeping and pathogenicity-related genes and virulence or avirulence towards the primary Malus resistance genes (R) has not been previously studied for Venturia inaequalis fungus, the causal agent of apple scab. In this study, the sequences of two housekeeping genes encoding elongation factor alpha (EF-1α) and β-tubulin and two previously unstudied effector genes of V. inaequalis from mannosidase and glucosidase families of 100 strains collected from apple cultivars with Rvi6, Rvi1, and Rvi17 and without known scab resistance genes were submitted to the analyses. Based on the phylogenetic and diversity data, as well as recombination analyses of the sequenced regions, we assessed the phylogenetic relationships and genetic structure of the pathogen within the species and the evolutionary forces that are currently acting upon this microorganism. The topology of the obtained phylograms demonstrates the lack of a relationship between the phylogenetic position of the strain and the host cultivar and the geographical origin or race of the strain. The isolates from different hosts were differentiated but did not form diagnosable, distinct phylogenetic groups. These results suggest that the analyzed genes may be too conserved to reflect the adaptation of pathogens to apple genotypes with different R genes; thus, they do not adequately reflect race discrimination. In contrast, based on variation and gene flow estimation, genetic divergence was observed among strains virulent to apple trees containing Rvi6. The results of this study confirmed a lack of free recombination between strains and demonstrated that the analyzed regions are in linkage disequilibrium and contain non-random polymorphisms associated with the strain.

Highlights

Apples are among the most economically important fruit tree crops in temperate zones, including Poland
It has been shown that Rvi6 cultivars divide V. inaequalis populations into two genetically different subgroups, Rvi6-virulent and Rvi6-avirulent, while this structuring effect was not observed for other R genes
The topologies of the trees representing all the regions and combined datasets were similar in the NJ and Bayesian analyses; only NJ trees are presented (Figure 1a–f), with bootstrap values being shown for well-supported branches and Bayesian posterior probability values (Bpp) values being given for co-occurring nodes

Summary

Introduction

Apples are among the most economically important fruit tree crops in temperate zones, including Poland. Several studies have obtained evidence that some races of the fungus possess unique genetic patterns recognized as an effect of strong selection pressure exerted by the host, as has been widely reported for the Rvi apple gene [6,7,8,9,10,11]. It has been shown that Rvi cultivars divide V. inaequalis populations into two genetically different subgroups, Rvi6-virulent (named race 6) and Rvi6-avirulent, while this structuring effect was not observed for other R genes. It is assumed that two pathogen lines exist: populations able to or not able to affect Rvi hosts, respectively. These presumably diverged and were separated by distance long time ago [10]. The influence of the apple genotype, including the main resistance genes (in this instance, Rvi, Rvi or Rvi1), on other genomic regions of V. inaequalis, including the core genome with housekeeping genes or genes encoding pathogenesis-related proteins, has not been studied to date

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