Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen Phytophthora infestans.

The plant pathogen that caused the Irish potato famine, Phytophthora infestans, continues to reemerge globally. These modern epidemics are caused by clonally reproducing lineages. In contrast, a sexual mode of reproduction is observed at its center of origin in Mexico. We conducted a comparative genomic analysis of 47 high-coverage genomes to infer changes in genic copy number. We included samples from sexual populations at the center of origin as well as several dominant clonal lineages sampled worldwide. We conclude that sexual populations at the center of origin are diploid, as was the lineage that caused the famine, while modern clonal lineages showed increased copy number (3×). Copy number variation (CNV) was found genome-wide and did not to adhere to the two-speed genome hypothesis. Although previously reported, tetraploidy was not found in any of the genomes evaluated. We propose a model of dominant clone emergence supported by the epidemiological record (e.g., EU_13_A2, US-11, US-23) whereby a higher copy number provides fitness, leading to replacement of prior clonal lineages.IMPORTANCE The plant pathogen implicated in the Irish potato famine, Phytophthora infestans, continues to reemerge globally. Understanding changes in the genome during emergence can provide insights useful for managing this pathogen. Previous work has relied on studying individuals from the United States, South America, Europe, and China reporting that these can occur as diploids, triploids, or tetraploids and are clonal. We studied variation in sexual populations at the pathogen's center of origin, in Mexico, where it has been reported to reproduce sexually as well as within clonally reproducing, dominant clones from the United States and Europe. Our results newly show that sexual populations at the center of origin are diploid, whereas populations elsewhere are more variable and show genome-wide variation in gene copy number. We propose a model of evolution whereby new pathogen clones emerge predominantly by increasing the gene copy number genome-wide.

Variation in Genetic Diversity of Phytophthora infestans Populations in Mexico from the Center of Origin Outwards.

The Toluca valley, located in central Mexico, is thought to be the center of origin of the potato late blight pathogen Phytophthora infestans. We characterized over 500 individuals of P. infestans sampled from populations with a geographical distance of more than 400 km in six regions adjacent to the Toluca valley in three states including Michoacán, Mexico, and Tlaxcala. Our sampling occurred on a predominant east to west gradient and showed significant genetic differentiation. The most western sampling location found in Michoacán was most differentiated from the other populations. Populations from San Gerónimo, Juchitepec, and Tlaxcala clustered together and appeared to be in linkage equilibrium. This work provides a finer understanding of gradients of genetic diversity in populations of P. infestans at the center of origin.

High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin.

Globally destructive crop pathogens often emerge by migrating out of their native ranges. These pathogens are often diverse at their centre of origin and may exhibit adaptive variation in the invaded range via multiple introductions from different source populations. However, source populations are generally unidentified or poorly studied compared to invasive populations. Phytophthora infestans, the causal agent of late blight, is one of the most costly pathogens of potato and tomato worldwide. Mexico is the centre of origin and diversity of P. infestans and migration events out of Mexico have enormously impacted disease dynamics in North America and Europe. The debate over the origin of the pathogen, and population studies of P. infestans in Mexico, has focused on the Toluca Valley, whereas neighbouring regions have been little studied. We examined the population structure of P. infestans across central Mexico, including samples from Michoacán, Tlaxcala and Toluca. We found high levels of diversity consistent with sexual reproduction in Michoacán and Tlaxcala and population subdivision that was strongly associated with geographic region. We determined that population structure in central Mexico has contributed to diversity in introduced populations based on relatedness of U.S. clonal lineages to Mexican isolates from different regions. Our results suggest that P. infestans exists as a metapopulation in central Mexico, and this population structure could be contributing to the repeated re-emergence of P. infestans in the United States and elsewhere.

Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology.

Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study were US-8 (n = 28), US-11 (n = 27), US-23 (n = 166), and US-24 (n = 36), with isolates originating from 23 of the United States and Ontario, Canada. The majority of isolates were collected between 2010 and 2014 (94%), with the remaining isolates collected from 1994 to 2009, and 2015. Between 3,774 and 5,070 single-nucleotide polymorphisms (SNPs) were identified within each lineage and were used to investigate relationships among individuals. K-means hierarchical clustering revealed three clusters within lineage US-23, with US-23 isolates clustering more by collection year than by geographic origin. K-means hierarchical clustering did not reveal significant clustering within the smaller US-8, US-11, and US-24 data sets. Neighbor-joining (NJ) trees were also constructed for each lineage. All four NJ trees revealed evidence for pathogen dispersal and overwintering within regions, as well as long-distance pathogen transport across regions. In the US-23 NJ tree, grouping by year was more prominent than grouping by region, which indicates the importance of long-distance pathogen transport as a source of initial late blight inoculum. Our results support previous studies that found significant genetic diversity within clonal lineages of P. infestans and show that GBS offers sufficiently high resolution to detect sub-structuring within clonal populations.

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes.

Phytophthora infestans is a destructive plant pathogen best known for causing the disease that triggered the Irish potato famine and remains the most costly potato pathogen to manage worldwide. Identification of P. infestan's elusive center of origin is critical to understanding the mechanisms of repeated global emergence of this pathogen. There are two competing theories, placing the origin in either South America or in central Mexico, both of which are centers of diversity of Solanum host plants. To test these competing hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches to unraveling complex demographic histories. Our analyses used microsatellite markers and sequences of four nuclear genes sampled from populations in the Andes, Mexico, and elsewhere. To infer the ancestral state, we included the closest known relatives Phytophthora phaseoli, Phytophthora mirabilis, and Phytophthora ipomoeae, as well as the interspecific hybrid Phytophthora andina. We did not find support for an Andean origin of P. infestans; rather, the sequence data suggest a Mexican origin. Our findings support the hypothesis that populations found in the Andes are descendants of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well documented as centers of evolution and diversity for numerous crop plants, the number of plant pathogens with a known geographic origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as the harnessing of plant disease resistance to manage late blight.

Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen.

Pest and pathogen losses jeopardise global food security and ever since the 19(th) century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.

The plant pathogen Phytophthora andina emerged via hybridization of an unknown Phytophthora species and the Irish potato famine pathogen, P. infestans.

Emerging plant pathogens have largely been a consequence of the movement of pathogens to new geographic regions. Another documented mechanism for the emergence of plant pathogens is hybridization between individuals of different species or subspecies, which may allow rapid evolution and adaptation to new hosts or environments. Hybrid plant pathogens have traditionally been difficult to detect or confirm, but the increasing ease of cloning and sequencing PCR products now makes the identification of species that consistently have genes or alleles with phylogenetically divergent origins relatively straightforward. We investigated the genetic origin of Phytophthora andina, an increasingly common pathogen of Andean crops Solanum betaceum, S. muricatum, S. quitoense, and several wild Solanum spp. It has been hypothesized that P. andina is a hybrid between the potato late blight pathogen P. infestans and another Phytophthora species. We tested this hypothesis by cloning four nuclear loci to obtain haplotypes and using these loci to infer the phylogenetic relationships of P. andina to P. infestans and other related species. Sequencing of cloned PCR products in every case revealed two distinct haplotypes for each locus in P. andina, such that each isolate had one allele derived from a P. infestans parent and a second divergent allele derived from an unknown species that is closely related but distinct from P. infestans, P. mirabilis, and P. ipomoeae. To the best of our knowledge, the unknown parent has not yet been collected. We also observed sequence polymorphism among P. andina isolates at three of the four loci, many of which segregate between previously described P. andina clonal lineages. These results provide strong support that P. andina emerged via hybridization between P. infestans and another unknown Phytophthora species also belonging to Phytophthora clade 1c.

Quantitative resistance to late blight from Solanum berthaultii cosegregates with R(Pi-ber): insights in stability through isolates and environment.

Genetic resistance is a valuable tool in the fight against late blight of potatoes but little is known about the stability and specificity of quantitative resistance including the effect of defeated major resistance genes. In the present study we investigated the effect of different isolates of Phytophthora infestans on the mode of action of R(Pi-ber), an R-gene originating from Solanum berthaultii. The experiments were conducted on progenies derived from two reciprocal inter-specific backcrosses of Solanum tuberosum and S. berthaultii. The plant-pathogen interaction was tested in diverse environments including field, greenhouse and growth chamber conditions. The R(Pi-ber) gene provided complete resistance against a US8 isolate of P. infestans in all trials. When isolates compatible with R(Pi-ber) were used for inoculation, a smaller, but significant resistance effect was consistently detected in the same map position as the R-gene. This indicates that this R-gene provides a residual resistance effect, and/or that additional resistance loci are located in this genomic region of chromosome X. Additional quantitative resistance loci (QRL) were identified in the analyzed progenies. While some of the QRL (such as those near TG130 on chromosome III) were effective against several isolates of the pathogen, others were isolate specific. With a single exception, the S. berthaultii alleles were associated with a decrease in disease severity. Resistance loci reported in the present study co-locate with previously reported R-genes and QRL to P. infestans and other pathogens.

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.

The biology of Phytophthora infestans at its center of origin.

The central highlands of Mexico are considered to be a center of genetic diversity for both the potato late blight pathogen and for tuber-bearing Solanum spp. Recent work conducted in Mexico and South America sheds new light on the biology and evolution of Phytophthora infestans and other related Phytophthora pathogens. It now appears that Mexican Solanum species, which coevolved with P. infestans and were previously known for providing a source of R-genes, also provide a source of quantitative, rate-reducing resistance that is highly effective, stable, and durable. It is now apparent that Mexico is the center of origin not only of the potato late blight pathogen P. infestans, but also of several related Phytophthora species including P. mirabilis, P. ipomoeae, and possibly P. phaseoli. We close with the hypothesis that these Phytophthora species evolved sympatrically from one ancestral host through adaptive radiation onto their respective four host families.