Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Abstract

The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.

Phytophthora: an ancient, historic, biologically and structurally cohesive and evolutionarily successful generic concept in need of preservation

“…Above all, the major Phytophthora clades are still confirmed to be a relatively tight, bush-like, fundamentally monophyletic, evolutionary cluster. Indeed Clades 9 and 10, considered by Cooke et al ( 2000 ) to be more distant, are now more closely aligned with the other major clades (Jung et al 2017c ; Yang et al 2017 ; Scanu et al 2021 ; Van Poucke et al 2021 ; Chen et al 2022 ). This is in contrast to the oomycete genus Pythium which, beginning with Cooke et al ( 2000 ), has been shown to be evolutionarily divergent and polyphyletic, and in consequence was split into several monophyletic genera (de Cock et al 2015 ; Uzuhashi et al 2010 ).…”

“…Clade structure sustained Göker et al ( 2007 ) 2009 400–600 Phytophthora species predicted Brasier ( 2009 ) 2014 Divergence of Phytophthora Clades predicted at 19.8–39 m years ago Matari and Blair ( 2014 ) 2017 Designation of Nothophytophthora gen. nov. Phytophthora origin pre the Gondwana-Laurasia separation (> 180 Myr) proposed Jung et al ( 2017a ) 2018 Multiple evolution of downy mildews from Phytophthoras demonstrated Bourret et al ( 2018 ) 2021 First phylogeny from genome-wide sequencing. Clade structure sustained Van Poucke et al ( 2021 ) 2021 Phytophthora reaches 200 described species Scanu et al ( 2021 ), Chen et al ( 2022 ) …”

“…Since then, at least 12 other molecular phylogenetic studies of Phytophthora have been undertaken, ranging from increasingly complex multigene analyses (Martin and Tooley 2003 ; Kroon et al 2004 , 2012 ; Blair et al 2008 ; Robideau et al 2011 ; Martin et al 2014 ; Rahman et al 2015 ; Jung et al 2017c ; Yang et al 2017 ; Bourret et al 2018 ; Scanu et al 2021 ; Chen et al 2022 ) to a genome-wide sequence-based phylogeny (Van Poucke et al 2021 ). These studies have been carried out against the background of the rapidly increasing number of described Phytophthora species outlined above.…”

“…Whisson et al 1994 ) and an outcrossing system (A1/A2 compatibility or ‘heterothallism’) that also enables selfing (Sansome 1980 ; Brasier 1992 ; Judelson 2009 ); (4) an ability to rapidly modify host–pathogen recognition processes via effector molecules (Kamoun et al 1997 ; Kamoun 2006 ) and other pathogenicity factors associated with the more rapidly evolving component of the ‘two speed’ genome (Raffaele and Kamoun 2012 ; Zhang et al 2019 ; Dale et al 2019 ); (5) rapid evolution of asexual clones via mitotic recombination and transposon induced mutagenesis (e.g. Kasuga et al 2016 ; Dale et al 2019 ); and (6) rapid evolution via interspecific hybridisation (Brasier et al 1999 , 2004 ; Man in’t Veldt et al 2012 ; Bertier et al 2013 ; Burgess 2015 ; Aguayo et al 2016 ; Jung et al 2017d ; Van Poucke et al 2021 ). These attributes may have facilitated adaptation to new hosts and new biogeographic environments without significant biological change; often resulting in convergent evolution between otherwise geographically isolated clades (Figs.…”

“…The narrower host and nutrient specificity, reduction in the effector repertoire and consistently reduced pathogenicity gene complements of the DMs (Fletcher et al 2018 ) could render DM species more prone to extinction in a changing environment (Thines and Choi 2016 ). Equally, by completing their life cycles in the more sheltered and homogeneous milieu of living plant tissues DMs are probably less exposed to competition from other microorganisms; and due to their host specificity at less ‘risk’ of interspecific hybridisation, especially compared with the ecologically more flexible Phytophthoras (Brasier 2001 ; Van Poucke et al 2021 ).…”