Molecular Phylogenomics and Population Structure of Phytophthora pluvialis

Abstract

Phytophthora pluvialis is an oomycete that was first isolated from soil, water, and tree foliage in mixed Douglas-fir - tanoak forests of the US Pacific Northwest (PNW). It was then identified as the causal agent of red needle cast (RNC) of radiata pine (Pinus radiata) in New Zealand (NZ). Genotyping-by-sequencing (GBS) was used to obtain 1,543 single nucleotide polymorphisms (SNPs) across 145 P. pluvialis isolates to characterize the population structure in the PNW and NZ. We tested the hypothesis that P. pluvialis was introduced to NZ from the PNW using genetic distance measurements and population structure analyzes among locations between countries, . The low genetic distance, population heterozygosity, and lack of geographic structure in NZ, suggest a single colonization event from the US followed by clonal expansion in NZ. The PNW Coast Range was proposed as a presumptive center of origin of the currently known distribution of P. pluvialis based on its geographic range and position as the central cluster in a minimum spanning network. The Coastal cluster of isolates were located at the root of every US cluster, and emerged earlier than all NZ clusters. The Coastal cluster had the highest degree of heterozygosity (Hs = 0.254) and median pairwise genetic distance (0.093) relative to any other cluster. Finally, the rapid host diversification between closely related isolates of P. pluvialis in New Zealand, indicate that this pathogen has the potential to infect a broader range of hosts than is currently recognized.

Urban environments harbor greater oomycete and Phytophthora diversity, creating a bridgehead for potential new pathogens to natural ecosystems

“…The impact of anthropogenic activities and patterns of invasion on plant pathogen communities is still poorly understood, partly because of their cryptic nature (Fisher et al, 2012). For some prominent invasive tree pathogens, global distribution and genetic structure follow patterns of human-mediated dispersal rather than natural dispersal (Brar et al, 2018;Dutech et al, 2012;Grünwald et al, 2012Grünwald et al, , 2019Keriö et al, 2020;LeBlanc et al, 2020;Sakalidis et al, 2016;Tabima et al, 2019Tabima et al, , 2020.…”

Spatial Genetic Structure of the Insect-Vectored Conifer Pathogen Leptographium wageneri Suggests Long Distance Gene Flow Among Douglas-fir Plantations in Western Oregon

“…Many studies examining the epidemiology of forest diseases have focused on invasive pathogens (Goss et al, 2009;Garbelotto et al, 2013;Barnes et al, 2014;Brar et al, 2015;Bennett et al, 2019;Tabima et al, 2021) but there are relatively few studies that have focused on investigating the factors influencing the population structure of native insect-vectored conifer pathogens. The influences of landscape-level dispersal dynamics on population structure, described herein, provide insights into the epidemiology of Lw var.…”

“…Previous studies examining the epidemiology of BSRD have focused on trapping and identifying the insects that spread the fungus that causes the disease (Harrington et al, 1985;Witcosky and Hansen, 1985). However, population genetics and genomics have become valuable tools to investigate the epidemiology and dispersal dynamics of both native and introduced plant pathogens (Linde et al, 2002(Linde et al, , 2009Rivas et al, 2004;Banke and McDonald, 2005;Goss et al, 2009;Rieux et al, 2011;Garbelotto et al, 2013;Barnes et al, 2014;Brar et al, 2015Brar et al, , 2018Grünwald et al, 2016;Bennett et al, 2019;Tabima et al, 2020Tabima et al, , 2021. Information about population structure and genetic diversity is essential for understanding how factors such as landscape topology or forest management practices influence the epidemiology and evolutionary biology of pathogens and for developing effective strategies for managing plant diseases (Linde et al, 2002Banke and McDonald, 2005;Heinzelmann et al, 2012;McDonald and Mundt, 2016).…”

Efficacy and optimal timing of low-volume aerial applications of copper fungicides for the control of red needle cast of pine

“…Both Phytophthora species associated with RNC are also found associated with other host species and in other regions of the World. Phytophthora pluvialis is thought to be native to the Pacific Northwest region of North America (Brar et al 2018;Tabima et al 2021), where it was first described from cultures isolated from stream, soil and canopy drip baitings in mixed tanoak-Douglas fir (Notholithocarpus densiflorus (Hook. & Arn.)…”