Globally invading populations of the fungal plant pathogen Verticillium dahliae are dominated by multiple divergent lineages

Abstract

The spread of aggressive fungal pathogens into previously non-endemic regions is a major threat to plant health and food security. Analyses of the spatial and genetic structure of plant pathogens offer valuable insights into their origin, dispersal mechanisms and evolution, and have been useful to develop successful disease management strategies. Here, we elucidated the genetic diversity, population structure and demographic history of worldwide invasion of the ascomycete Verticillium dahliae, a soil-borne pathogen, using a global collection of 1100 isolates from multiple plant hosts and countries. Seven well-differentiated genetic clusters were revealed through discriminant analysis of principal components (DAPC), but no strong associations between these clusters and host/geographic origin of isolates were found. Analyses of clonal evolutionary relationships among multilocus genotypes with the eBURST algorithm and analyses of genetic distances revealed that genetic clusters represented several ancient evolutionary lineages with broad geographic distribution and wide host range. Comparison of different scenarios of demographic history using approximate Bayesian computations revealed the branching order among the different genetic clusters and lineages. The different lineages may represent incipient species, and this raises questions with respect to their evolutionary origin and the factors allowing their maintenance in the same areas and same hosts without evidence of admixture between them. Based on the above findings and the biology of V. dahliae, we conclude that anthropogenic movement has played an important role in spreading V. dahliae lineages. Our findings have implications for the development of management strategies such as quarantine measures and crop resistance breeding.

Comparison of genotyping by sequencing and microsatellite markers for unravelling population structure in the clonal fungus Verticillium dahliae

“…For example, Short et al . () directly labelled the forward primer with a fluorescent dye, as opposed to the method here using labelled M13 primers (Schuelke, ; Dung et al ., ).…”

“…() because they reported alleles in terms of number of repeats per locus, not fragment size, as done in this study and reported by Short et al . ().…”

“…(), 18 nt were first subtracted from each allele size to account for the M13 sequence added to each forward primer; Short et al . () fluorescently labelled one PCR primer for each marker. Allele sizes from the two laboratories were compared based on the most common alleles observed within clusters and lineages, under the assumption that the most common alleles would be the same in both samples.…”

“…In addition, the same isolate in both studies (W83, a potato isolate from USA) was genotyped, together with one isolate in this study (4TM6‐15, from cotton in China), which was from the same collection as an isolate in the Short et al . () study (4TM6‐24), to compare allele sizes.…”

“…The objectives of the present study were: (i) to compare microsatellite genotyping on isolates previously genotyped by GBS from known clonal lineages to determine if it is possible to assign isolates to clonal lineages using microsatellite markers; (ii) to determine the correspondence of genotype clusters identified from microsatellite genotyping by Short et al . () with clonal lineages defined by GBS and VCGs (Milgroom et al ., ); (iii) to test whether isolates identified as race 1 (Short et al ., ) are in lineage 2A, as reported by Jiménez‐Díaz et al . (); (iv) to test whether microsatellite genotyping shows greater variation within the 1A/D clonal lineage causing olive wilt epidemics in Spain than that shown by GBS (Milgroom et al ., ); and (v) to test if there is any evidence of recombination within and between lineages based on microsatellite data.…”