The origins of plant pathogens in agro-ecosystems

Disease-reducing effect of Chromolaena odorata extract on sheath blight and other rice diseases

Sheath blight caused by Rhizoctonia solani (teleomorph: Thanatephorus cucumeris) is a major cause of crop loss in intensive rice production systems. No economically viable control methods have been developed. We screened aqueous extracts of common herbal plants that could reduce sheath blight lesions and found that foliar spraying and seed soaking application of extracts of either fresh or dried leaves of Chromolaena odorata gave up to 68% reduction in sheath blight lesion lengths under controlled and semi-field conditions. The observed reductions were not dependent on growth conditions of C. odorata and rice cultivar. The effect was observed until 21 days after inoculation and was not dependent on microbial activity. Under semi-field conditions, extracts also reduced severity of other important rice diseases, i.e., blast (Pyricularia oryzae) using foliar spray (up to 45%), brown spot (Bipolaris oryzae) using seed treatment (up to 57%), and bacterial blight (Xanthomonas oryzae pv. oryzae) using both application methods (up to 50%).

Plant-parasite coevolution: bridging the gap between genetics and ecology

We review current ideas about coevolution of plants and parasites, particularly processes that generate genetic diversity. Frequencies of host resistance and parasite virulence alleles that interact in gene-for-gene (GFG) relationships coevolve in the familiar boom-and-bust cycle, in which resistance is selected when virulence is rare, and virulence is selected when resistance is common. The cycle can result in stable polymorphism when diverse ecological and epidemiological factors cause negative direct frequency-dependent selection (ndFDS) on host resistance, parasite virulence, or both, such that the benefit of a trait to fitness declines as its frequency increases. Polymorphism can also be stabilized by overdominance, when heterozygous hosts have greater resistance than homozygotes to diverse pathogens. Genetic diversity can also persist in the form of statistical polymorphism, sustained by random processes acting on gene frequencies and population size. Stable polymorphism allows alleles to be long-lived and genetic variation to be detectable in natural populations. In agriculture, many of the factors promoting stability in host-parasite interactions have been lost, leading to arms races of host defenses and parasite effectors.

Variation in pathogenicity and aggressiveness of Erysiphe necator from different Vitis spp. and geographic origins in the eastern United States

Eastern North America is considered the center of diversity for many Vitis spp. and for the grape powdery mildew pathogen, Erysiphe necator. However, little is known about populations of E. necator from wild Vitis spp. We determined the phenotypic variation in pathogenicity and aggressiveness of E. necator among isolates from wild and domesticated Vitis spp. from diverse geographic regions in the eastern United States. To test pathogenicity, we inoculated 38 E. necator isolates on three wild Vitis spp., two commercially grown hybrids and the European wine grape, Vitis vinifera. V. rotundifolia (muscadine grape) was the only host species on which complete host specialization was evident; it was only susceptible to isolates collected from V. rotundifolia. All isolates, regardless of source host, were pathogenic on the other Vitis spp. We found no differences in components of aggressiveness latent period and lesion size among isolates from different source hosts when inoculated on V. vinifera, which is highly susceptible to powdery mildew. However significant variation was evident among isolates on the more resistant V. labruscana 'Niagara'. Isolates from the wild species V. aestivalis were the most aggressive, whereas isolates from V. vinifera were not more aggressive than isolates from other source hosts. Greater aggressiveness was also detected among isolates from the southeastern United States compared with isolates from the northeastern United States.

Genetic structure of Phytophthora infestans populations in China indicates multiple migration events

One hundred isolates of Phytophthora infestans collected from 10 provinces in China between 1998 and 2004 were analyzed for mating type, metalaxyl resistance, mitochondrial DNA (mtDNA) haplotype, allozyme genotype, and restriction fragment length polymorphism (RFLP) with the RG-57 probe. In addition, herbarium samples collected in China, Russia, Australia, and other Asian countries were also typed for mtDNA haplotype. The Ia haplotype was found during the first outbreaks of the disease in China (1938 and 1940), Japan (1901, 1930, and 1931), India (1913), Peninsular Malaysia (1950), Nepal (1954), The Philippines (1910), Australia (1917), Russia (1917), and Latvia (1935). In contrast, the Ib haplotype was found after 1950 in China on both potato and tomato (1952, 1954, 1956, and 1982) and in India (1968 and 1974). Another migration of a genotype found in Siberia called SIB-1 (Glucose-6-phosphate isomerase [Gpi] 100/100, Peptidase [Pep] 100/100, IIa mtDNA haplotype) was identified using RFLP fingerprints among 72% of the isolates and was widely distributed in the north and south of China and has also been reported in Japan. A new genotype named CN-11 (Gpi 100/111, Pep 100/100, IIb mtDNA haplotype), found only in the south of China, and two additional genotypes (Gpi 100/100, Pep 100/100, Ia mtDNA haplotype) named CN-9 and CN-10 were identified. There were more diverse genotypes among isolates from Yunnan province than elsewhere. The SIB-1 (IIa) genotype is identical to those from Siberia, suggesting later migration of this genotype from either Russia or Japan into China. The widespread predominance of SIB-1 suggests that this genotype has enhanced fitness compared with other genotypes found. Movement of the pathogen into China via infected seed from several sources most likely accounts for the distribution of pathogen genotypes observed. MtDNA haplotype evidence and RFLP data suggest multiple migrations of the pathogen into China after the initial introduction of the Ia haplotype in the 1930s.

Host range, biological variation, and phylogenetic diversity of Eutypa lata in California

The objectives of this study were to investigate the host range of Eutypa lata in the major grape-growing regions in California and to analyze the phenotypic variation and phylogenetic diversity of E. lata isolates. Perithecia of E. lata were found on grapevines, in apricot, almond, cherry, apple, and pear tree orchards, and on ornamentals (oleander) and native plant species (California buckeye, big leaf maple, and willow). Multigene phylogenies of ribosomal DNA internal transcribed spacer, β-tubulin, and RPB2 genes confirmed the identity of E. lata recovered from the various host plants but also revealed sequence differences among isolates. The intraspecific phylogenetic diversity of E. lata did not correspond to geography or source of isolation, and intraspecific groups were not consistent across the different DNA phylogenies. Significant phenotypic variation also was detected among E. lata isolates, including ascospore and conidium length as well as level of aggressiveness on grapevines. Pathogenicity studies proved that all isolates were infectious to grapevine, suggesting that the native vegetation surrounding vineyards can serve as inoculum sources that may constitute an important element in the epidemiology of Eutypa dieback in grapevines.

Pathogenesis, parasitism and mutualism in the trophic space of microbe-plant interactions

Microbe-host interactions can be categorised as pathogenic, parasitic or mutualistic, but in practice few examples exactly fit these descriptions. New molecular methods are providing insights into the dynamics of microbe-host interactions, with most microbes changing their relationship with their host at different life-cycle stages or in response to changing environmental conditions. Microbes can transition between the trophic states of pathogenesis and symbiosis and/or between mutualism and parasitism. In plant-based systems, an understanding of the true ecological niche of organisms and the dynamic state of their trophic interactions with their hosts has important implications for agriculture, including crop rotation, disease control and risk management.

Genetic diversity of the mating type and toxin production genes in Pyrenophora tritici-repentis

Pyrenophora tritici-repentis, the causal agent of tan spot on wheat, is a homothallic loculoascomycete with a complex race structure. The objectives of this study were to confirm the homothallic nature of the pathogen, characterize mating type diversity and toxin production genes in a global collection of strains, and analyze how these traits are associated between each other and with existing races. The pseudothecia production capacity, race identification, mating type locus (MAT), internal transcribed spacer, and glyceraldehyde-3-phosphate dehydrogenase regions were analyzed in a selection of 88 strains originating from Europe, North and South America, North Africa, and Central and South Asia. Some (60%) strains produced pseudothecia containing ascospores, independent of their origin. Race identification obtained using the multiplex polymerase chain reaction targeting host-selective toxin (HST) genes was consistent, overall, with the results based on the inoculation of a set of differential wheat cultivars and confirmed the predominance of race 1/2 strains ( approximately 83%). However, discrepancies in race identification, differences from the reference tester strains, and atypical ToxA profiles suggest the presence of new races and HSTs. The MAT1-1 and MAT1-2 coding regions are consecutively arranged in a single individual, suggesting putative heterothallic origin of P. tritici-repentis. Upstream from the MAT is an open reading frame of unknown function (ORF1) containing a MAT-specific degenerate carboxy-terminus. The phylogenetic analysis of the MAT locus reveals two distinct groups, unlinked to geographical origin or ToxA profile. Group I, the best-represented group, is associated with typical tan spot lesions caused by races 1, 2, 3, and 5 on wheat. It is more homogenous than group II encompassing race 4 strains, as well as isolates associated primarily with small spot lesions on wheat leaves or other hosts. Group II could contain several distinct taxa.

Linking the emergence of fungal plant diseases with ecological speciation

Emerging diseases represent a growing worldwide problem accompanying global environmental changes. There is tremendous interest in identifying the factors controlling the appearance and spread of these diseases. Here, we discuss emerging fungal plant diseases, and argue that they often result from host shift speciation (a particular case of ecological speciation). We consider the factors controlling local adaptation and ecological speciation, and show that certain life-history traits of many fungal plant pathogens are conducive for rapid ecological speciation, thus favoring the emergence of novel pathogen species adapted to new hosts. We argue that placing the problem of emerging fungal diseases of plants within the context of ecological speciation can significantly improve our understanding of the biological mechanisms governing the emergence of such diseases.

Microsatellite markers reveal two admixed genetic groups and an ongoing displacement within the French population of the invasive plant pathogen Phytophthora infestans

Potato late blight is an example of a re-emerging disease of plants. Phytophthora infestans was first introduced into Europe during the 19th century, where it caused the Irish potato famine. During the 20th century several additional introduction events have been suspected, especially in the mid-70s due to the import of large quantities of potato needed after the shortage caused by drought in 1976. Here, we investigate the genetic population structure of Phytophthora infestans, at the first stages of a recent invasion process in France. A total of 220 isolates was collected from 20 commercial fields of the potato susceptible cultivar Bintje, during two consecutive years (2004 and 2005). Clustering analyses based on eight recently developed microsatellite markers reveal that French P. infestans populations are made of two differentiated genetic clusters of isolates (F(ST) = 0.19). This result suggests multiple introductions of P. infestans into France, either through the introduction of a composite population of isolates or through the successive introduction of isolates having differentiated genetic backgrounds. Both clusters identified have a strong clonal structure and are similar regarding genetic diversity and mating type composition. The maintenance of differentiation between the two genetic clusters should result from the low or non-existent contribution of sexual reproduction in French P. infestans populations.

Phakopsora pachyrhizi, the causal agent of Asian soybean rust

The plant pathogenic basidiomycete fungi Phakopsora pachyrhizi and Phakopsora meibomiae cause rust disease in soybean plants. Phakopsora pachyrhizi originated in Asia-Australia, whereas the less aggressive P. meibomiae originated in Latin America. In the New World, P. pachyrhizi was first reported in the 1990s to have spread to Hawaii and, since 2001, it has been found in South America. In 2004, the pathogen entered continental USA. This review provides detailed information on the taxonomy and molecular biology of the pathogen, and summarizes strategies to combat the threat of this devastating disease.

TAXONOMY

Phakopsora pachyrhizi Syd. & P. Syd; uredial anamorph: Malupa sojae (syn. Uredo sojae); Domain Eukaryota; Kingdom Fungi; Phylum Basidiomycota; Order Uredinales; Class Urediniomycetes; Family Phakopsoraceae; Genus Phakopsora (http://www.indexfungorum.org). The nomenclature of rust spores and spore-producing structures used within this review follows Agrios GN (2005) Plant Pathology, 5th edn. London: Elsevier/Academic Press.

HOST RANGE

In the field, P. pachyrhizi infects leaf tissue from a broad range (at least 31 species in 17 genera) of leguminous plants. Infection of an additional 60 species in other genera has been achieved under laboratory conditions.

DISEASE SYMPTOMS

At the beginning of the disease, small, tan-coloured lesions, restricted by leaf veins, can be observed on infected soybean leaves. Lesions enlarge and, 5-8 days after initial infection, rust pustules (uredia, syn. uredinia) become visible. Uredia develop more frequently in lesions on the lower surface of the leaf than on the upper surface. The uredia open with a round ostiole through which uredospores are released.

Sclerotia of Typhula ishikariensis biotype B (Typhulaceae) from archaeological sites (4000 to 400 BP) in Hokkaido, northern Japan

Despite their close association with human activities, plant pathogenic fungi have rarely been found in archaeological excavations. We report here that a fungus was closely associated with human activities even in prehistoric times. Sclerotium-like objects were found at historical sites (4000 to 400 BP) on the island of Hokkaido, northern Japan. They were spherical, 0.3-1.0 mm in diameter, and had a medulla and rind. Some had leaf fragments on the surface or a protuberance that resembled emerging sporocarp primordia. These traits indicated that they were sclerotia of the snow mold fungus, Typhula ishikariensis biotype B.

Divergence between sympatric rice- and maize-infecting populations of Rhizoctonia solani AG-1 IA from Latin America

ABSTRACT The basidiomycetous fungus Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen in Latin America causing sheath blight (SB) of rice. Particularly in Venezuela, the fungus also causes banded leaf and sheath blight (BLSB) on maize, which is considered an emerging disease problem where maize replaced traditional rice-cropping areas or is now planted in adjacent fields. Our goals in this study were to elucidate (i) the effects of host specialization on gene flow between sympatric and allopatric rice and maize-infecting fungal populations and (ii) the reproductive mode of the fungus, looking for evidence of recombination. In total, 375 isolates of R. solani AG1 IA sampled from three sympatric rice and maize fields in Venezuela (Portuguesa State) and two allopatric rice fields from Colombia (Meta State) and Panama (Chiriquí State) were genotyped using 10 microsatellite loci. Allopatric populations from Venezuela, Colombia, and Panama were significantly differentiated (Phi(ST) of 0.16 to 0.34). Partitioning of the genetic diversity indicated differentiation between sympatric populations from different host species, with 17% of the total genetic variation distributed between hosts while only 3 to 6% was distributed geographically among the sympatric Venezuelan fields. We detected symmetrical historical migration between the rice- and the maize-infecting populations from Venezuela. Rice- and maize-derived isolates were able to infect both rice and maize but were more aggressive on their original hosts, consistent with host specialization. Because the maize- and rice-infecting populations are still cross-pathogenic, we postulate that the genetic differentiation was relatively recent and mediated via a host shift. An isolation with migration analysis indicated that the maize-infecting population diverged from the rice-infecting population between 40 and 240 years ago. Our findings also suggest that maize-infecting populations have a mainly recombining reproductive system whereas the rice-infecting populations have a mixed reproductive system in Latin America.

Quantitative resistance increases the durability of qualitative resistance to Leptosphaeria maculans in Brassica napus

It has frequently been hypothesized that quantitative resistance increases the durability of qualitative (R-gene mediated) resistance but supporting experimental evidence is rare. To test this hypothesis, near-isogenic lines with/without the R-gene Rlm6 introduced into two Brassica napus cultivars differing in quantitative resistance to Leptosphaeria maculans were used in a 5-yr field experiment. Recurrent selection of natural fungal populations was done annually on each of the four plant genotypes, using crop residues from each genotype to inoculate separately the four series of field trials for five consecutive cropping seasons. Severity of phoma stem canker was measured on each genotype and frequencies of avirulence alleles in L. maculans populations were estimated. Recurrent selection of virulent isolates by Rlm6 in a susceptible background rendered the resistance ineffective by the third cropping season. By contrast, the resistance was still effective after 5 yr of selection by the genotype combining this gene with quantitative resistance. No significant variation in the performance of quantitative resistance alone was noted over the course of the experiment. We conclude that quantitative resistance can increase the durability of Rlm6. We recommend combining quantitative resistance with R-gene mediated resistance to enhance disease control and crop production.

Ecological genetic divergence of the fungal pathogen Didymella rabiei on sympatric wild and domesticated Cicer spp. (Chickpea)

For millennia, chickpea (Cicer arietinum) has been grown in the Levant sympatrically with wild Cicer species. Chickpea is traditionally spring-sown, while its wild relatives germinate in the autumn and develop in the winter. It has been hypothesized that the human-directed shift of domesticated chickpea to summer production was an attempt to escape the devastating Ascochyta disease caused by Didymella rabiei. We estimated genetic divergence between D. rabiei isolates sampled from wild Cicer judaicum and domesticated C. arietinum and the potential role of temperature adaptation in this divergence. Neutral genetic markers showed strong differentiation between pathogen samples from the two hosts. Isolates from domesticated chickpea demonstrated increased adaptation to higher temperatures when grown in vitro compared with isolates from the wild host. The distribution of temperature responses among progeny from crosses of isolates from C. judaicum with isolates from C. arietinum was continuous, suggesting polygenic control of this trait. In vivo inoculations of host plants indicated that pathogenic fitness of the native isolates was higher than that of their hybrid progeny. The results indicate that there is a potential for adaptation to higher temperatures; however, the chances for formation of hybrids which are capable of parasitizing both hosts over a broad temperature range are low. We hypothesize that this pathogenic fitness cost is due to breakdown of coadapted gene complexes controlling pathogenic fitness on each host and may be responsible for maintenance of genetic differentiation between the pathogen demes.

Genes acquired by horizontal transfer are potentially involved in the evolution of phytopathogenicity in Moniliophthora perniciosa and Moniliophthora roreri, two of the major pathogens of cacao

Moniliophthora perniciosa and Moniliophthora roreri are phytopathogenic basidiomycete species that infect cacao causing two important diseases in this crop: "Witches' Broom" and "Frosty Pod Rot", respectively. The ability of species from this genus (Moniliophthora) to cause disease is exceptional in the family Marasmiaceae. Species in closely related genera including, Marasmius, Crinipellis, and Chaetocalathus, are mainly saprotrophs and are not known to cause disease. In this study, the possibility that this phytopathogenic lifestyle has been acquired by horizontal gene transfer (HGT) was investigated. A stringent genome comparison pipeline was used to identify potential genes that have been obtained by Moniliophthora through HGT. This search led to the identification of three genes: a metallo-dependent hydrolase (MDH), a mannitol phosphate dehydrogenase (MPDH), and a family of necrosis-inducing proteins (NEPs). Phylogenetic analysis of these genes suggests that Moniliophthora acquired NEPs from oomycetes, MDH from actinobacteria and MPDH from firmicutes. Based on the known gene functions and on previous studies of M. perniciosa infection and development, a correlation between gene acquisition and the evolution of the phytopathogenic genus Moniliophthora can be postulated.

Genetic isolation among sympatric vegetative compatibility groups of the aflatoxin-producing fungus Aspergillus flavus

Aspergillus flavus, a fungal pathogen of animals and both wild and economically important plants, is most recognized for producing aflatoxin, a cancer-causing secondary metabolite that contaminates food and animal feed globally. Aspergillus flavus has two self/nonself recognition systems, a sexual compatibility system and a vegetative incompatibility system, and both play a role in directing gene flow in populations. Aspergillus flavus reproduces clonally in wild and agricultural settings, but whether a cryptic sexual stage exists in nature is currently unknown. We investigated the distribution of genetic variation in 243 samples collected over 4 years from three common vegetative compatibility groups (VCGs) in Arizona and Texas from cotton using 24 microsatellite loci and the mating type locus (MAT) to assess population structure and potential gene flow among A. flavus VCGs in sympatric populations. All isolates within a VCG had the same mating type with OD02 having MAT1-2 and both CG136 and MR17 having MAT1-1. Our results support the hypothesis that these three A. flavus VCGs are genetically isolated. We found high levels of genetic differentiation and no evidence of gene flow between VCGs, including VCGs of opposite mating-type. Our results suggest that these VCGs diverged before domestication of agricultural hosts (>10,000 yr bp).

Wheat domestication accelerated evolution and triggered positive selection in the beta-xylosidase enzyme of Mycosphaerella graminicola

Plant cell wall degrading enzymes (PCWDEs) of plant pathogens are receiving increasing interest for their potential to trigger plant defense reactions. In an antagonistic co-evolutionary arms race between host and pathogen, PCWDEs could be under strong selection. Here, we tested the hypothesis that PCWDEs in the fungal wheat pathogen Mycosphaerella graminicola have been positively selected by analyzing ratios of non-synonymous and synonymous nucleotide changes in the genes encoding these enzymes. Analyses of five PCWDEs demonstrated that one (beta-xylosidase) has been under strong positive selection and experienced an accelerated rate of evolution. In contrast, PCWDEs in the closest relatives of M. graminicola collected from wild grasses did not show evidence for selection or deviation from a molecular clock. Since the genealogical divergence of M. graminicola from these latter species coincided with the onset of agriculture, we hypothesize that the recent domestication of the host plant and/or agricultural practices triggered positive selection in beta-xylosidase and that this enzyme played a key role in the emergence of a host-specialized pathogen.

Combating plant diseases--the Darwin connection

Although Darwin knew of plant diseases, he did not study them as part of his analysis of natural selection. Effective plant disease control has only been developed after his death. This article explores the relevance of Darwin's ideas to three problem areas with respect to diseases caused by fungi: emergence of new diseases, loss of disease resistance bred into plants and development of fungicide resistance. Darwin's concept of change through natural or artificial selection relied on selection of many small changes, but subsequent genetic research has shown that change can also occur through large steps. Appearance of new diseases can involve gene duplication, transfer or recombination, but all evidence points to both host plant resistance and fungicide susceptibility being overcome through point mutations. Because the population size of diseases such as rusts and powdery and downy mildews is so large, all possible point mutations are likely to occur daily, even during moderate epidemics. Overcoming control measures therefore reflects the overall fitness of these mutants, and much resource effort is being directed towards assessment of their fitness, both in the presence and in the absence of selection. While recent developments in comparative genomics have caused some revision of Darwin's ideas, experience in managing plant disease control measures clearly demonstrates the relevance of concepts he introduced 150 years ago. It also reveals the remarkable speed and the practical impact of adaptation in wild microorganism populations to changes in their environment, and the difficulty of stopping or delaying such adaptation.

Gene transfer and diversification of microbial eukaryotes

The importance of lateral gene transfer in genome evolution of microbial eukaryotes is slowly being appreciated. Acquisitions of genes have led to metabolic adaptation in diverse eukaryotic lineages. In most cases the metabolic genes have originated from prokaryotes, often followed by sequential transfers between eukaryotes. However, the knowledge of gene transfer in eukaryotes is still mainly based on anecdotal evidence. Some of the observed patterns may be biases in experimental approaches and sequence databases rather than evolutionary trends. Rigorous systematic studies of gene acquisitions that allow for the possibility of exchanges of all categories of genes from all sources are needed to get a more objective view of gene transfer in eukaryote evolution. It may be that the role of gene transfer in the diversification process of microbial eukaryotes currently is underestimated.

Genetic structure of populations of the rice-infecting pathogen Rhizoctonia solani AG-1 IA from China

ABSTRACT Sheath blight disease (SBD) on rice, caused by Rhizoctonia solani AG-1 IA, is one of the most devastating rice diseases on a global basis, including China (in Eastern Asia), the world's largest rice-growing country. We analyzed the population genetics of nine rice-infecting populations from China using nine microsatellite loci. One allopatric population from India (Southern Asia) was included in the analyses. In total, 300 different multilocus genotypes were found among 572 fungal isolates. Clonal fractions within rice fields were 16 to 95%, suggesting that sclerotia were a major source of primary inoculum in some fields. Global Phi(ST) statistics (Phi(ST) = 42.49; P </= 0.001) were consistent with a relatively high level of differentiation among populations overall; however, pairwise comparisons gave nonsignificant R(ST) values, consistent with contemporary gene flow among five of the populations. Four of these populations were located along the Yangtze River tributary network. Gene flow followed an isolation-by-distance model consistent with restricted long-distance migration. Historical migration rates were reconstructed and yielded values that explained the current levels of population subdivision. Except for one population which appeared to be strictly clonal, all populations showed evidence of a mixed reproductive mode, including both asexual and sexual reproduction. One population had a strictly recombining structure (all loci were in Hardy-Weinberg equilibrium) but the remaining populations from China and the one from India exhibited varying degrees of sexual reproduction. Six populations showed significant F(IS) values consistent with inbreeding.

Population genetics of fungal and oomycete effectors involved in gene-for-gene interactions

Antagonistic coevolution between plants and pathogens has generated a broad array of attack and defense mechanisms. In the classical avirulence (Avr) gene-for-gene model, the pathogen gene evolves to escape host recognition while the host resistance (R) gene evolves to track the evolving pathogen elicitor. In the case of host-specific toxins (HST), the evolutionary arms race may be inverted, with the gene encoding the pathogen toxin evolving to maintain recognition of the host sensitivity target while the host sensitivity gene evolves to escape binding with the toxin. Pathogen effector genes, including those encoding Avr elicitors and HST, often show elevated levels of polymorphism reflecting the coevolutionary arms race between host and pathogen. However, selection can also eliminate variation in the coevolved gene and its neighboring regions when advantageous alleles are swept to fixation. The distribution and diversity of corresponding host genes will have a major impact on the distribution and diversity of effectors in the pathogen population. Population genetic analyses including both hosts and their pathogens provide an essential tool to understand the diversity and dynamics of effector genes. Here, we summarize current knowledge about the population genetics of fungal and oomycete effector genes, focusing on recent studies that have used both spatial and temporal collections to assess the diversity and distribution of alleles and to monitor changes in allele frequencies over time. These studies illustrate that effector genes exhibit a significant degree of diversity at both small and large sampling scales, suggesting that local selection plays an important role in their evolution. They also illustrate that Avr elicitors and HST may be recognizing the same R genes in plants, leading to evolutionary outcomes that differ for necrotrophs and biotrophs while affecting the evolution of the corresponding R genes. Under this scenario, the optimal number of R genes in a plant genome may be determined by the relative abundance of necrotrophic and biotrophic pathogens in the plant's environment.

Recent evolution of bacterial pathogens: the gall-forming Pantoea agglomerans case

Pantoea agglomerans, a widespread epiphyte and commensal bacterium, has evolved into an Hrp-dependent and host-specific tumorigenic pathogen by acquiring a plasmid containing a pathogenicity island (PAI). The PAI was evolved on an iteron plasmid of the IncN family, which is distributed among genetically diverse populations of P. agglomerans. The structure of the PAI supports the premise of a recently evolved pathogen. This review offers insight into a unique model for emergence of new bacterial pathogens. It illustrates how horizontal gene transfer was the major driving force in the creation of the PAI, although a pathoadaptive mechanism might also be involved. It describes the crucial function of plant-produced indole-3-acetic acid (IAA) and cytokinines (CK) in gall initiation as opposed to the significant but secondary role of pathogen-secreted phytohormones. It also unveils the role of type III effectors in determination of host specificity and evolution of the pathogen into pathovars. Finally, it describes how interactions between the quorum sensing system, hrp regulatory genes, and bacterially secreted IAA or CKs affect gall formation and epiphytic fitness.