Evidence for homoploid speciation in Phytophthora alni supports taxonomic reclassification in this species complex

Abstract

Alder decline has been a problem along European watercourses since the early 1990s. Hybridization was identified as the main cause of this emerging disease. Indeed, the causal agent, a soil-borne pathogen named Phytophthora alni subsp. alni (Paa) is the result of interspecific hybridization between two taxa, Phytophthora alni subsp. multiformis (Pam) and Phytophthora alni subsp. uniformis (Pau), initially identified as subspecies of Paa. The aim of this work was to characterize the ploidy level within the P. alni complex that is presently poorly understood. For that, we used two complementary approaches for a set of 31 isolates of Paa, Pam and Pau: (i) quantification of allele copy number of three single-copy nuclear genes using allele-specific real-time PCR and (ii) comparison of the genome size estimated by flow cytometry. Relative quantification of alleles of the three single-copy genes showed that the copy number of a given allele in Paa was systematically half that of its parents Pau or Pam. Moreover, DNA content estimated by flow cytometry in Paa was equal to half the sum of those in Pam and Pau. Our results therefore suggest that the hybrid Paa is an allotriploid species, containing half of the genome of each of its parents Pam and Pau, which in turn are considered to be allotetraploid and diploid, respectively. Paa thus results from a homoploid speciation process. Based on published data and on results from this study, a new formal taxonomic name is proposed for the three taxa Paa, Pam and Pau which are raised to species status and renamed P. ×alni, P. ×multiformis and P. uniformis, respectively.

The plasticity of fungal interactions

“…Adapting the species concept to include hybridization is a more general problem also, emphasized in cases of oomycotan fungal analogues (Husson et al 2015). Recently, Husson et al (2015) have described the hybridization between two subspecies with different ploidies and the appearance of a new hybrid subspecies.…”

“…Recently, Husson et al (2015) have described the hybridization between two subspecies with different ploidies and the appearance of a new hybrid subspecies. The authors found that the new hybrid DNA was equal to half the sum of the parental DNAs, but one parental genome was tetraploid while the second was diploid.…”

Genetic diversity and genetic structure of black alder (Alnus glutinosa [L.] Gaertn) in the Belgium-Luxembourg-France cross-border area

“…Since the early 1990s, it has been endangered by the hybrid oomycete Phytophthora ×alni, leading to dieback in riparian ecosystems (Husson et al 2015). This pathogen is the result of interspecific hybridization between two taxa, P. uniformis and P. ×multiformis.…”

Genetic Diversity and Origins of the Homoploid-Type Hybrid Phytophthora ×alni

“…Phytophthora uniformis and Phytophthora ϫmultiformis have been identified as the parents of P. ϫalni (15,16). Recent work coupling flow cytometry and quantification of allele copy number determined the exact ploidy levels of the three species of the complex (17). Accordingly, P. ϫalni was shown to be a triploid homoploid-type taxon that formed through the hybridization of a diploid taxon (P. uniformis) and a tetraploid taxon (P. ϫmultiformis) without chromosome doubling.…”