Genetic structure of Pyrenophora teres net and spot populations as revealed by microsatellite analysis

Leišová‐Svobodová, Leona; Minarikova, V.; Matušinsky, Pavel; Hudcovicová, Martina; Ondreičková, Katarína; Gubiš, Jozef

doi:10.1016/j.funbio.2013.11.008

Cited by 15 publications

(8 citation statements)

References 42 publications

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“…PTM appears to have spread since, being noted in Australia in 1977 ( Khan and Tekauz, 1982 ) and in Montana, United States in 1981 ( Bockelman et al, 1983 ). Although artificial hybrids can be readily made in the laboratory ( McDonald, 1967 ; Smedegård-Petersen, 1977a ; Campbell and Crous, 2003 ; Jalli, 2011 ), PTT and PTM are considered to be genetically autonomous populations ( Rau et al, 2003 , 2007 ; Bakonyi and Justesen, 2007 ; Bogacki et al, 2010 ; Lehmensiek et al, 2010 ; Leišová-Svobodová et al, 2014 ; Akhavan et al, 2016 ). Natural hybrids appear to be rare and have been suggested by RAPD and AFLP studies ( Campbell et al, 2002 ; Leišova et al, 2005 ; McLean et al, 2014 ), and recently confirmed by Poudel et al (2017) using form-specific markers.…”

Section: Introductionmentioning

confidence: 99%

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

et al. 2018

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Pyrenophora teres, P. teres f. teres (PTT) and P. teres f. maculata (PTM) cause significant diseases in barley, but little is known about the large-scale genomic differences that may distinguish the two forms. Comprehensive genome assemblies were constructed from long DNA reads, optical and genetic maps. As repeat masking in fungal genomes influences the final gene annotations, an accurate and reproducible pipeline was developed to ensure comparability between isolates. The genomes of the two forms are highly collinear, each composed of 12 chromosomes. Genome evolution in P. teres is characterized by genome fissuring through the insertion and expansion of transposable elements (TEs), a process that isolates blocks of genic sequence. The phenomenon is particularly pronounced in PTT, which has a larger, more repetitive genome than PTM and more recent transposon activity measured by the frequency and size of genome fissures. PTT has a longer cultivated host association and, notably, a greater range of host–pathogen genetic interactions compared to other Pyrenophora spp., a property which associates better with genome size than pathogen lifestyle. The two forms possess similar complements of TE families with Tc1/Mariner and LINE-like Tad-1 elements more abundant in PTT. Tad-1 was only detectable as vestigial fragments in PTM and, within the forms, differences in genome sizes and the presence and absence of several TE families indicated recent lineage invasions. Gene differences between P. teres forms are mainly associated with gene-sparse regions near or within TE-rich regions, with many genes possessing characteristics of fungal effectors. Instances of gene interruption by transposons resulting in pseudogenization were detected in PTT. In addition, both forms have a large complement of secondary metabolite gene clusters indicating significant capacity to produce an array of different molecules. This study provides genomic resources for functional genetics to help dissect factors underlying the host–pathogen interactions.

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Section: Introductionmentioning

confidence: 99%

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

et al. 2018

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“…Microsatellites, or simple sequence repeats (SSRs), are single sequence motifs comprising no more than six bases that are tandem repeated (Lei sov a-Svobodov a et al, 2014). SSRs are popular as genetic markers due to their high reproducibility, multiallelic nature, co-dominant mode of inheritance, abundance and wide genome coverage, and they have proved helpful for genetic characterization of fungi (Garbelotto et al, 2013;Lei sov a-Svobodov a et al, 2014;Gonthier et al, 2015). Two steps are critical for the use of SSR markers in population genetics studies.…”

Section: Introductionmentioning

confidence: 99%

HRM analysis provides insights on the reproduction mode and the population structure of Gnomoniopsis castaneae in Europe

et al. 2016

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Gnomoniopsis castaneae is an emergent nut rot agent of chestnut in southern Europe. To elucidate its population genetics, three simple sequence repeat (SSR) and two hypervariable markers were developed and assessed through high‐resolution melting (HRM) analysis on 132 isolates collected from 10 sites in Italy, France and Switzerland. High allele diversity (ranging from 0.23 to 0.40 depending on site) and number of haplotypes (49) were observed. More than 70% of the molecular variance could be accounted among isolates within sites. Multilocus analysis showed absence of linkage disequilibrium, suggesting a predominant role played by sexual reproduction and random mating. Data analyses indicated the presence of at least two putative distinct subpopulations and this was confirmed by several approaches, including analysis of shared haplotypes, multivariate and Bayesian analyses. Based on data of allelic diversity, the possibility that the pathogen could have been introduced is discussed. This work assessed the genetic variability and the sexual strategies of G. castaneae in Europe, adding useful information on the epidemiology of this fungal plant pathogen.

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“…Leišová‐Svobodová et al . () used similar Bayesian clustering with isolates from the Czech Republic and found limited admixture between most sampling locations, although both unique and admixtured clusters occurred. Significant genetic differentiation was found using AMOVA among the northern and southern groups over a two‐year period (Φ PT = 0.25, P = 0.001 or 25% of genetic diversity among groups and 75% within groups) with less but still significant variance over a three‐year period (Φ PT = 0.17, P = 0.002).…”

Section: Discussionmentioning

confidence: 97%

“…PTT is therefore an obligate outcrossing fungus, resulting in genetically diverse populations (Rau et al, 2003(Rau et al, , 2005Liu et al, 2012;Akhavan et al, 2016a,b). Genetic differences between populations have been observed regionally within Sardinia, the Czech Republic and over intercontinental distances (Rau et al, 2003;Serenius et al, 2007;Lehmensiek et al, 2010;Lei sov a-Svobodov a et al, 2014).…”

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confidence: 99%

Genetic variation of Pyrenophora teres f. teres isolates in Western Australia and emergence of a Cyp51A fungicide resistance mutation

et al. 2018

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Genome‐wide, unlinked, simple sequence repeat markers were used to examine genetic variation and relationships within Pyrenophora teres f. teres, a common pathogen of barley, in Western Australia. Despite the region's geographic isolation, the isolates showed relatively high allelic variation compared to similar studies, averaging 7.11 alleles per locus. Principal component, Bayesian clustering and distance differentiation parameters provided evidence for both regional genotypic subdivision together with juxtaposing of isolates possessing different genetic backgrounds. Genotyping of fungicide resistant Cyp51A isolates indicated a single mutation event occurred followed by recombination and long‐distance regional dispersal over hundreds of kilometres. Selection of recently emergent favourable alleles such as the Cyp51A mutation and a cultivar virulence may provide an explanation, at least in part, for juxtaposed genotypes. Factors affecting genotypic composition and the movement of new genotypes are discussed in the context of grower practices and pathogen epidemiology, together with the implications for resistance breeding.

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Genetic structure of Pyrenophora teres net and spot populations as revealed by microsatellite analysis

Cited by 15 publications

References 42 publications

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

HRM analysis provides insights on the reproduction mode and the population structure of Gnomoniopsis castaneae in Europe

Genetic variation of Pyrenophora teres f. teres isolates in Western Australia and emergence of a Cyp51A fungicide resistance mutation

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