Diversity of Virulence in Phytophthora parasitica on Tobacco, as Reflected by Nuclear RFLPs

Neofunctionalization of Glycolytic Enzymes: An Evolutionary Route to Plant Parasitism in the Oomycete Phytophthora nicotianae

Oomycetes, of the genus Phytophthora, comprise of some of the most devastating plant pathogens. Parasitism of Phytophthora results from evolution from an autotrophic ancestor and adaptation to a wide range of environments, involving metabolic adaptation. Sequence mining showed that Phytophthora spp. display an unusual repertoire of glycolytic enzymes, made of multigene families and enzyme replacements. To investigate the impact of these gene duplications on the biology of Phytophthora and, eventually, identify novel functions associated to gene expansion, we focused our study on the first glycolytic step on P. nicotianae, a broad host range pathogen. We reveal that this step is committed by a set of three glucokinase types that differ by their structure, enzymatic properties, and evolutionary histories. In addition, they are expressed differentially during the P. nicotianae life cycle, including plant infection. Last, we show that there is a strong association between the expression of a glucokinase member in planta and extent of plant infection. Together, these results suggest that metabolic adaptation is a component of the processes underlying evolution of parasitism in Phytophthora, which may possibly involve the neofunctionalization of metabolic enzymes.

Characterization of Two Satellite DNA Families in the Genome of the Oomycete Plant Pathogen Phytophthora parasitica

Satellite DNA is a class of repetitive sequences that are organized in long arrays of tandemly repeated units in most eukaryotes. Long considered as selfish DNA, satellite sequences are now proposed to contribute to genome integrity. Despite their potential impact on the architecture and evolution of the genome, satellite DNAs have not been investigated in oomycetes due to the paucity of genomic data and the difficulty of assembling highly conserved satellite arrays. Yet gaining knowledge on the structure and evolution of genomes of oomycete pathogens is crucial to understanding the mechanisms underlying adaptation to their environment and to proposing efficient disease control strategies. A de novo assembly of the genome of Phytophthora parasitica, an important oomycete plant pathogen, led to the identification of several families of tandemly repeated sequences varying in size, copy number, and sequence conservation. Among them, two abundant families, designated as PpSat1 and PpSat2, displayed typical features of satellite DNA and were collectively designated as PpSat. These two satellite families differ by their length, sequence, organization, genomic environment, and evolutionary dynamics. PpSat1, but not PpSat2, presented homologs among oomycetes. This observation, as well as the characterization of transcripts of PpSat families, suggested that these satellite DNA families likely play a conserved role within this important group of pathogens.

Population Structure of Phytophthora nicotianae Reveals Host-Specific Lineages on Brinjal, Ridge Gourd, and Tomato in South India

Severe outbreaks of Phytophthora fruit rot on brinjal, ridge gourd, and tomato have been observed since 2011 in Andhra Pradesh, Karnataka, Telangana, and Tamil Nadu states of India. Therefore, 76 Phytophthora nicotianae isolates, recovered from brinjal (17), ridge gourd (40), and tomato (19) from different localities in these states during the June to December cropping season of 2012 and 2013, were characterized based on phenotypic and genotypic analyses and aggressiveness on brinjal, tomato, and ridge gourd. All brinjal and ridge gourd isolates were A2, while tomato isolates were both A1 (13) and A2 (6). All isolates were metalaxyl sensitive. In addition, isolates were genotyped for three mitochondrial (ribosomal protein L5-small subunit ribosomal RNA [rpl5-rns], small subunit ribosomal RNA-cytochrome c oxidase subunit 2 [rns-cox2], and cox2+spacer) and three nuclear loci (hypothetical protein [hyp], scp-like extracellular protein [scp], and beta-tubulin [β-tub]). All regions were polymorphic but nuclear regions were more variable than mitochondrial regions. The network analysis of genotypes using the combined dataset of three nuclear regions revealed a host-specific association. However, the network generated using mitochondrial regions limited such host-specific groupings only to brinjal isolates. P. nicotianae isolates were highly aggressive and produced significantly (P ≤ 0.01) larger lesions on their respective host of origin than on other hosts. The results indicate significant genetic variation in the population of P. nicotianae, leading to identification of host-specific lineages responsible for severe outbreaks on brinjal, ridge gourd, and tomato.

Genetic Analysis of Phytophthora nicotianae Populations from Different Hosts Using Microsatellite Markers

In all, 231 isolates of Phytophthora nicotianae representing 14 populations from different host genera, including agricultural crops (Citrus, Nicotiana, and Lycopersicon), potted ornamental species in nurseries (Lavandula, Convolvulus, Myrtus, Correa, and Ruta), and other plant genera were characterized using simple-sequence repeat markers. In total, 99 multilocus genotypes (MLG) were identified, revealing a strong association between genetic grouping and host of recovery, with most MLG being associated with a single host genus. Significant differences in the structure of populations were revealed but clonality prevailed in all populations. Isolates from Citrus were found to be genetically related regardless of their geographic origin and were characterized by high genetic uniformity and high inbreeding coefficients. Higher variability was observed for other populations and a significant geographical structuring was determined for isolates from Nicotiana. Detected differences were related to the propagation and cultivation systems of different crops. Isolates obtained from Citrus spp. are more likely to be distributed worldwide with infected plant material whereas Nicotiana and Lycopersicon spp. are propagated by seed, which would not contribute to the spread of the pathogen and result in a greater chance for geographic isolation of lineages. With regard to ornamental species in nurseries, the high genetic variation is likely the result of the admixture of diverse pathogen genotypes through the trade of infected plant material from various geographic origins, the presence of several hosts in the same nursery, and genetic recombination through sexual reproduction of this heterothallic species.

The Top 10 oomycete pathogens in molecular plant pathology

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.

Analyses of the population structure in a global collection of Phytophthora nicotianae isolates inferred from mitochondrial and nuclear DNA sequences

Genetic variation within the heterothallic cosmopolitan plant pathogen Phytophthora nicotianae was determined in 96 isolates from a wide range of hosts and geographic locations by characterizing four mitochondrial (10% of the genome) and three nuclear loci. In all, 52 single-nucleotide polymorphisms (SNPs) (an average of 1 every 58 bp) and 313 sites with gaps representing 5,450 bases enabled the identification of 50 different multilocus mitochondrial haplotypes. Similarly, 24 SNPs (an average of 1 every 69 bp), with heterozygosity observed at each locus, were observed in three nuclear regions (hyp, scp, and β-tub) differentiating 40 multilocus nuclear genotypes. Both mitochondrial and nuclear markers revealed a high level of dispersal of isolates and an inconsistent geographic structuring of populations. However, a specific association was observed for host of origin and genetic grouping with both nuclear and mitochondrial sequences. In particular, the majority of citrus isolates from Italy, California, Florida, Syria, Albania, and the Philippines clustered in the same mitochondrial group and shared at least one nuclear allele. A similar association was also observed for isolates recovered from Nicotiana and Solanum spp. The present study suggests an important role of nursery populations in increasing genetic recombination within the species and the existence of extensive phenomena of migration of isolates that have been likely spread worldwide with infected plant material.

Genetic characterization of Phytophthora nicotianae by the analysis of polymorphic regions of the mitochondrial DNA

A new method based on the analysis of mitochondrial intergenic regions characterized by intraspecific variation in DNA sequences was developed and applied to the study of the plant pathogen Phytophthora nicotianae. Two regions flanked by genes trnY and rns and trnW and cox2 were identified by comparing the whole mitochondrial genomes of Phytophthora infestans, Phytophthora ramorum, and Phytophthora sojae and amplified using primers designed from the flanking conserved genes. These regions were sequenced from 51 isolates of P. nicotianae of both A1 and A2 mating type recovered from different hosts and geographic regions. Amplicon length varied from 429bp to 443bp (trnY/rns) and 322bp to 373bp (trnW/cox2) with intraspecific variation due to single nucleotide polymorphisms and indels. Seventeen, seven and 20 different haplotypes were detected by individually analyzing regions trnY-rns, trnW-cox2 and the combined data set of sequences from both regions, respectively. Phylogenetic analysis inferred with three different methods enabled the grouping of isolates in five clades, each containing different mitochondrial haplotypes and revealed diversity in the mitochondrial genome of P. nicotianae. The majority of isolates from citrus grouped in a single clade indicating either movement of isolates on planting stock or an association of particular isolates with this host. Phylogenetic groups were not correlated with the radial growth rate of the isolates or the rapidity of apple flesh colonization. The method developed in the present study represents an innovative molecular tool for the characterization of natural populations of P. nicotianae and should be easily expanded to other species of Phytophthora as well as other plant pathogens. It can be used to track specific haplotypes and, thanks to its high genetic resolution, it could be standardized and applied in a DNA barcoding like strategy for the precise identification of sub-specific taxa. Compared to alternative molecular methods, a major advantage is that results are unbiased (a list of nucleotides) and highly reproducible, thus enabling the comparison of data from different laboratories and time periods. Furthermore, the method could be further enhanced by the identification of additional variable mitochondrial and/or nuclear genomic regions.

An Assessment of the Genetic Diversity in a Field Population of Phytophthora nicotianae with a Changing Race Structure

One hundred fifty-three isolates of Phytophthora nicotianae that were collected over a 4-year period from a single field were subjected to amplified fragment length polymorphism (AFLP) analysis to investigate the effect of different types of resistance in tobacco (Nicotiana tabacum) on genetic diversity in the pathogen population. No race 1 isolates were detected in the field prior to initiating the study, but the race was present in multiple plots by the end of the 4-year period. There were 102 race 0 isolates and 51 race 1 isolates characterized. Seventy-six of the 153 isolates had a unique AFLP profile, whereas the remaining 77 isolates were represented by 27 AFLP profiles shared by at least two isolates. Isolates of both races were found in both the unique and shared AFLP profile groups. Twenty-three of the AFLP profiles were detected in multiple years, indicating a clonal component to the pathogen population. Race 1 isolates that were detected over multiple years were always obtained from the same plot. No race 1 profile was found in more than one plot, confirming the hypothesis that the multiple occurrences of the race throughout the field were the result of independent events and not pathogen spread. Three identical race 0 AFLP profiles occurred in noncontiguous plots, and in each case, the plots contained the same partially resistant variety. Cluster analysis provided a high level of bootstrap support for 41 isolates in 19 clusters that grouped primarily by race and rotation treatment. Estimates of genetic diversity ranged from 0.365 to 0.831 and varied depending on tobacco cultivar planted and race. When averaged over all treatments, diversity in race 1 isolates was lower than in race 0 isolates at the end of each season. Deployment of single-gene resistance initially decreased genetic diversity of the population, but the diversity increased each year, indicating the pathogen was adapting to the host genotypes deployed in the field.

Influence of Pythium oligandrum biocontrol on fungal and oomycete population dynamics in the rhizosphere

Fungal and oomycete populations and their dynamics were investigated following the introduction of the biocontrol agent Pythium oligandrum into the rhizosphere of tomato plants grown in soilless culture. Three strains of P. oligandrum were selected on the basis of their ability to form oospores (resting structures) and to produce tryptamine (an auxin-like compound) and oligandrin (a glycoprotein elicitor). Real-time PCR and plate counting demonstrated the persistence of large amounts of the antagonistic oomycete in the rhizosphere throughout the cropping season (April to September). Inter-simple-sequence-repeat analysis of the P. oligandrum strains collected from root samples at the end of the cropping season showed that among the three strains used for inoculation, the one producing the smallest amount of oospores was detected at 90%. Single-strand conformational polymorphism analysis revealed increases in the number of members and the complexity of the fungal community over time. There were no significant differences between the microbial ecosystems inoculated with P. oligandrum and those that were not treated, except for a reduction of Pythium dissotocum (ubiquitous tomato root minor pathogen) populations in inoculated systems during the last 3 months of culture. These findings raise interesting issues concerning the use of P. oligandrum strains producing elicitor and auxin molecules for plant protection and the development of biocontrol.

Exploration of the late stages of the tomato-Phytophthora parasitica interactions through histological analysis and generation of expressed sequence tags

The oomycete Phytophthora parasitica is a soilborne pathogen infecting numerous plants. The infection process includes an initial biotrophic stage, followed by a necrotrophic stage. The aim here was to identify genes that are involved in the late stages of infection. Using the host tomato and a transformed strain of P. parasitica expressing the green fluorescent protein (GFP), the various infection steps from recognition of the host to the colonization of plant tissues were studied. This late stage was selected to generate 4000 ESTs (expressed sequence tags), among which approx. 80% were from the pathogen. Comparison with an EST data set created previously from in vitro growth of P. parasitica allowed the identification of several genes, the expression of which might be regulated during late stages of infection. Changes in gene expression of several candidate genes predicted from in silico analysis were validated by quantitative RT-PCR experiments. These results give insights into the molecular bases of the necrotrophic stage of an oomycete pathogen.

Elicitin genes expressed in vitro by certain tobacco isolates of Phytophthora parasitica are down regulated during compatible interactions

Phytophthora spp. secrete proteins called elicitins in vitro that can specifically induce hypersensitive response and systemic acquired resistance in tobacco. In Phytophthora parasitica, the causal agent of black shank, most isolates virulent on tobacco are unable to produce elicitins in vitro. Recently, however, a few elicitin-producing P. parasitica strains virulent on tobacco have been isolated. We investigated the potential diversity of elicitin genes in P. parasitica isolates belonging to different genotypes and with various virulence levels toward tobacco as well as elicitin expression pattern in vitro and in planta. Although elicitins are encoded by a multigene family, parAl is the main elicitin gene expressed. This gene is highly conserved among isolates, regardless of the elicitin production and virulence levels toward tobacco. Moreover, we show that elicitin-producing P. parasitica isolates virulent on tobacco down regulate parAl expression during compatible interactions, whichever host plant is tested. Conversely, one elicitin-producing P. parasitica isolate that is pathogenic on tomato and avirulent on tobacco still expresses parAl in the compatible interaction. Therefore, some P. parasitica isolates may evade tobacco recognition by down regulating parA1 in planta. The in planta down regulation of parA1 may constitute a suitable mechanism for P. parasitica to infect tobacco without deleterious consequences for the pathogen.

Virulence and molecular diversity of parthenogenetic root-knot nematodes, Meloidogyne spp

Root-knot nematodes (RKN) are sedentary endoparasites causing severe damage to a wide variety of crops, including tomato. Among them, the parthenogenetic species Meloidogyne arenaria, M. incognita and M. javanica are of particular economic importance. The genetic diversity and relationships of 17 populations belonging to these three major species, either avirulent or virulent against the tomato Mi resistance gene, were investigated in order to determine whether (a)virulence of the nematodes could be related to their molecular fingerprints. Genomic polymorphisms between populations were assessed by using amplified fragment length polymorphism (AFLP) markers, and data were treated by means of a multiple correspondence analysis. A total of 1550 polymorphic amplified DNA fragments were identified and used to compute the relationships between the populations. As expected, the three RKN species were clearly distributed into distinct groups, but combination of data for virulence phenotypes and DNA markers showed that clustering of populations was not associated with their (a)virulence against the tomato Mi resistance gene. Such a lack of correlation indicates that most of the observed DNA polymorphism is independent of virulence, which is presumably under host selection. This result demonstrates that virulent populations do not share a common origin, and strongly suggests that they might have appeared late after the establishment of these clonal lineages, as the result of independent mutational events.