Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci

Real-time PCR quantification of Rhizoctonia solani AG-3 from soil samples

Rhizoctonia solani anastomosis group 3 (AG-3) causes several diseases of potato, including black scurf and stem canker, affecting potato production in the Skagit Valley, Washington, and around the world. Primers for a SYBR-Green II-based real-time polymerase chain reaction (qPCR) assay were designed from sequences of the nuclear internal transcribed spacer (ITS) regions of fungal isolates of potato and onion from the Pacific Northwest, USA. The primers preferentially amplified R. solani AG-3 DNA, compared to DNA from R. solani AG-4, AG-5 and AG-8. In silico analysis of primer-template duplex stability indicated that the assay also will detect R. solani AG-3 isolates from pea and onion in Washington State and from diverse crop species around the world, but not R. solani AG-9 and AG-2-1. The assay was used to quantify R. solani AG-3 populations in pathogen-infested field soils after temporary flooding rotation, a practice found to be effective for reducing Sclerotinia sclerotiorum and R. solani AG-3 in potatoes in growth chamber studies. Population densities of the pathogen were not significantly reduced in saturated (flooded) soils relative to fallow. However, the qPCR approach was more sensitive and quantitative than the toothpick baiting method for diagnosis of these soil samples. Accurate detection and quantification of R. solani AG-3 in soil will facilitate the development of integrated management plans for Rhizoctonia diseases of potato.

Genome-enabled analysis of plant-pathogen migration

Trade in plant and plant products has profoundly affected the global distribution and diversity of plant pathogens. Identification of migration pathways can be used to monitor or manage pathogen movement for proactive disease management or quarantine measures. Genomics-based genetic marker discovery is allowing unprecedented collection of population genetic data for plant pathogens. These data can be used for detailed analysis of the ancestry of population samples and therefore for analysis of migration. Reconstruction of migration histories has confirmed previous hypotheses based on observational data and led to unexpected new findings on the origins of pathogens and source populations for past and recent migration. The choice of software for analysis depends on the type of migration being studied and the reproductive mode of the pathogen. Biased sampling and complex population structures are potential challenges to accurate inference of migration pathways.

Molecular characterization and screening for sheath blight resistance using Malaysian isolates of Rhizoctonia solani

Two field isolates of Rhizoctonia solani were isolated from infected paddy plants in Malaysia. These isolates were verified via ITS-rDNA analysis that yielded ~720 bp products of the ITS1-5.8S-ITS4 region, respectively. The sequenced products showed insertion and substitution incidences which may result in strain diversity and possible variation in disease severity. These strains showed some regional and host-specific relatedness via Maximum Likelihood and further phylogenetic analysis via Maximum Parsimony showed that these strains were closely related to R. solani AG1-1A (with 99-100% identity). Subsequent to strain verification and analysis, these isolates were used in the screening of twenty rice varieties for tolerance or resistance to sheath blight via mycelial plug method where both isolates (1801 and 1802) showed resistance or moderate resistance to Teqing, TETEP, and Jasmine 85. Isolate 1802 was more virulent based on the disease severity index values. This study also showed that the mycelial plug techniques were efficient in providing uniform inoculum and humidity for screening. In addition this study shows that the disease severity index is a better mode of scoring for resistance compared to lesion length. These findings will provide a solid basis for our future breeding and screening activities at the institution.

Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3

The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi.

Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14

Anastomosis group AG1-IB isolates of the anamorphic basidiomycetous fungus Rhizoctonia solani Kühn affect various agricultural and horticultural important crops including bean, rice, soybean, figs, hortensia, cabbage and lettuce. To gain insights into the genome structure and content, the first draft genome sequence of R. solani AG1-IB isolate 7/3/14 was established. Four complete runs on the Genome Sequencer (GS) FLX platform (Roche Applied Science) yielding approx. a 25-fold coverage of the R. solani genome were accomplished. Assembly of the sequence reads by means of the gsAssembler software version 2.6 applying the heterozygotic mode resulted in numerous contigs and scaffolds and a predicted size of 87.1 Mb for the diploid status of the genome. 'Contig-length vs. read-count' analysis revealed that the assembled contigs can be classified into five different groups. Detailed BLAST-analysis revealed that most contigs of group II feature high-scoring matches to other contigs of the same group suggesting that distinguishable allelic variants exist for many genes. Due to the supposed diploid and heterokaryotic nature of R. solani AG1-IB 7/3/14, this result has been anticipated. However, the heterokaryotic character of the isolate is not really supported by sequencing data obtained for the isolate R. solani AG1-IB 7/3/14. Coverage of group III contigs is twice as high as for group II contigs which can also be explained by the diploid status of the genome and indistinguishable alleles on homologous chromosomes. Assembly of sequence data led to the identification of the rRNA unit (group V contigs) and the mitochondrial (mt) genome (group IV contigs) which is a circular molecule of 162,751 bp in size featuring a GC-content of 36.4%. The R. solani 7/3/14 mt-genome is one of the largest fungal mitochondrial genomes known to date. Its large size essentially is due to the presence of numerous non-conserved hypothetical ORFs and introns. Gene prediction for the R. solani AG1-IB 7/3/14 genome was conducted by the Augustus Gene Prediction Software for Eukaryotes (version 2.6.) applying the parameter set for the fungus Coprinopsis cinerea okayama 7#130. Gene prediction and annotation provided first insights into the R. solani AG1-IB 7/3/14 gene structure and content. In total, 12,422 genes were predicted. The average number of exons per gene is five. Exons have a mean length of 214 bp, whereas introns on average are 66 bp in length. Annotation of the genome revealed that 4169 of 12,422 genes could be assigned to KOG functional categories.

The population genetic structure of Rhizoctonia solani AG-3PT from potato in the Colombian Andes

The soilborne fungus Rhizoctonia solani anastomosis group 3 (AG-3PT) is a globally important potato pathogen. However, little is known about the population genetic processes affecting field populations of R. solani AG-3PT, especially in the South American Colombian Andes, which is near the center of diversity of the two most common groups of cultivated potato, Solanum tuberosum and S. phureja. We analyzed the genetic structure of 15 populations of R. solani AG-3PT infecting potato in Colombia using 11 simple-sequence repeat (SSR) markers. In total, 288 different multilocus genotypes were identified among 349 fungal isolates. Clonal fractions within field populations were 7 to 33%. RST statistics indicated a very low level of population differentiation overall, consistent with high contemporary gene flow, though moderate differentiation was found for the most distant southern populations. Genotype flow was also detected, with the most common genotype found widely distributed among field populations. All populations showed evidence of a mixed reproductive mode, including both asexual and sexual reproduction, but two populations displayed evidence of inbreeding.

Evidence that the Ceratobasidium-like white-thread blight and black rot fungal pathogens from persimmon and tea crops in the Brazilian Atlantic Forest agroecosystem are two distinct phylospecies

The white-thread blight and black rot (WTBR) caused by basidiomycetous fungi of the genus Ceratobasidium is emerging as an important plant disease in Brazil, particularly for crop species in the Ericales such as persimmon (Diospyros kaki) and tea (Camellia sinensis). However, the species identity of the fungal pathogen associated with either of these hosts is still unclear. In this work, we used sequence variation in the internal transcribed spacer regions, including the 5.8S coding region of rDNA (ITS-5.8S rDNA), to determine the phylogenetic placement of the local white-thread-blight-associated populations of Ceratobasidium sp. from persimmon and tea, in relation to Ceratobasidium species already described world-wide. The two sister populations of Ceratobasidium sp. from persimmon and tea in the Brazilian Atlantic Forest agroecosystem most likely represent distinct species within Ceratobasidium and are also distinct from C. noxium, the etiological agent of the first description of white-thread blight disease that was reported on coffee in India. The intraspecific variation for the two Ceratobasidium sp. populations was also analyzed using three mitochondrial genes (ATP6, nad1 and nad2). As reported for other fungi, variation in nuclear and mitochondrial DNA was incongruent. Despite distinct variability in the ITS-rDNA region these two populations shared similar mitochondrial DNA haplotypes.

Population biology of fungal plant pathogens

Studies of the population genetics of fungal and oomycetous phytopathogens are essential to clarifying the disease epidemiology and devising management strategies. Factors commonly associated with higher organisms such as migration, natural selection, or recombination, are critical for the building of a clearer picture of the pathogen in the landscape. In this chapter, we focus on a limited number of experimental and analytical methods that are commonly applied in population genetics. At first, we present different types of qualitative and quantitative traits that could be identified morphologically (phenotype). Subsequently, we describe several molecular methods based on dominant and codominant markers, and we provide our assessment of the advantages and shortfalls of these methods. Third, we discuss various analytical methods, which include phylogenies, summary statistics as well as coalescent-based methods, and we elaborate on the benefits associated with each approach. Last, we develop a case study in which we investigate the population structure of the fungal phytopathogen Verticillium dahliae in coastal California, and assess the hypotheses of transcontinental gene flow and recombination in a fungus that is described as asexual.

The adaptive potential of a plant pathogenic fungus, Rhizoctonia solani AG-3, under heat and fungicide stress

The ability to improve fitness via adaptive evolution may be affected by environmental change. We tested this hypothesis in an in vitro experiment with the plant pathogen Rhizoctonia solani Anastomosis Group 3 (AG-3), assessing genetic and environmental variances under two temperatures (optimal and higher than optimal) and three fungicide concentrations (no fungicide, low and high concentration of a copper-based fungicide). We measured the mean daily growth rate, the coefficient of variation for genotypic (I (G)) and environmental variance (I (E)) in growth, and broad-sense heritability in growth. Both higher temperature and increased fungicide concentration caused a decline in growth, confirming their potential as stressors for the pathogen. All types of standardized variances in growth-I (G), phenotypic variance, and I (E) as a trend-increased with elevated stress. However, heritability was not significantly higher under enhanced stress because the increase in I (G) was counterbalanced by somewhat increased I (E). The results illustrate that predictions for adaptation under environmental stress may depend on the type of short-term evolvability measure. Because mycelial growth is linked to fitness, I (G) reflects short-term evolvability better than heritability, and it indicates that the evolutionary potential of R. solani is positively affected by stress.

Genetic diversity of Rhizoctonia solani associated with potato tubers in France

The soilborne fungus Rhizoctonia solani is a pathogen of many plants and causes severe damage in crops around the world. Strains of R. solani from the anastomosis group (AG) 3 attack potatoes, leading to great yield losses and to the downgrading of production. The study of the genetic diversity of the strains of R. solani in France allows the structure of the populations to be determined and adapted control strategies against this pathogen to be established. The diversity of 73 French strains isolated from tubers grown in the main potato seed production areas and 31 strains isolated in nine other countries was assessed by phylogenetic analyses of (i) the internal transcribed spacer sequences (ITS1 and ITS2) of ribosomal RNA (rRNA), (ii) a part of the gene tef-1α and (iii) the total DNA fingerprints of each strain established by amplified fragment length polymorphism (AFLP). The determination of the AGs of R. solani based on the sequencing of the ITS region showed three different AGs among our collection (60 AG 3 PT, 8 AG 2-1 and 5 AG 5). Grouping of the strains belonging to the same AG was confirmed by sequencing of the gene tef-1α used for the first time to study the genetic diversity of R. solani. About 42% of ITS sequences and 72% of tef-1α sequences contained polymorphic sites, suggesting that the cells of R. solani strains contain several copies of ITS and the tef-1α gene within the same nucleus or between different nuclei. Phylogenetic trees showed a greater genetic diversity within AGs in tef-1α sequences than in ITS sequences. The AFLP analyses showed an even greater diversity among the strains demonstrating that the French strains of R. solani isolated from potatoes were not a clonal population. Moreover there was no relationship between the geographical origins of the strains or the variety from which they were isolated and their genetic diversity.

Molecular characterization of beta-tubulin from Phakopsora pachyrhizi, the causal agent of Asian soybean rust

β-tubulins are structural components of microtubules and the targets of benzimidazole fungicides used to control many diseases of agricultural importance. Intron polymorphisms in the intron-rich genes of these proteins have been used in phylogeographic investigations of phytopathogenic fungi. In this work, we sequenced 2764 nucleotides of the β-tubulin gene (Pp tubB) in samples of Phakopsora pachyrhizi collected from seven soybean fields in Brazil. Pp tubB contained an open reading frame of 1341 nucleotides, including nine exons and eight introns. Exon length varied from 14 to 880 nucleotides, whereas intron length varied from 76 to 102 nucleotides. The presence of only four polymorphic sites limited the usefulness of Pp tubB for phylogeographic studies in P. pachyrhizi. The gene structures of Pp tubB and orthologous β-tubulin genes of Melampsora lini and Uromyces viciae-fabae were highly conserved. The amino acid substitutions in β-tubulin proteins associated with the onset of benzimidazole resistance in model organisms, especially at His ₆ , Glu ₁₉₈ and Phe ₂₀₀ , were absent from the predicted sequence of the P. pachyrhizi β-tubulin protein.

Characterization of Diversity Among Isolates of Rhizoctonia oryzae-sativae from California Rice Fields

Thirty-one California isolates of Rhizoctonia oryzae-sativae, the cause of aggregate sheath spot of rice, were characterized by culture morphology, pathogenicity tests, somatic compatibility groups (SCGs), single-locus microsatellites (SLMs), and multilocus microsatellites (MLMs). The highest level of diversity (individual isolates) was described by MLMs whereas pathogenicity tests exhibited the lowest resolution. In general, a high degree of diversity was revealed (diversity from 51.6 to 100%) within the California population. Several lines of evidence indicated sexual reproduction in the population of R. oryzae-sativae. Genetic analyses of SLMs and MLMs revealed high genetic diversity and gametic equilibrium of all SLMs and most MLMs. Furthermore, unique individuals were recovered by MLMs and there was no correlation of phenotypes to either SCGs or genetic markers. In addition, incongruence of parsimonious trees generated from each of five primers of MLMs and a poorly resolved consensus tree inferred from the combined data set were demonstrated. Accordingly, sexual reproduction of R. oryzae-sativae is probably more prevalent in California than previously assumed.

An In Planta Method for Assessing the Role of Basidiospores in Rhizoctonia Foliar Disease of Tomato

A tomato (Solanum lycopersicum) foliar blight disease of unknown etiology was observed in North Carolina (NC) during 2005 to 2006. Symptoms included necrotic lesions and blighted leaves, with signs of white mycelial growth on abaxial leaf surfaces. The morphology of isolates from symptomatic leaves was consistent with that of Rhizoctonia solani. Because the pattern of symptom expression suggested that basidiospores were the primary inoculum source, Koch's postulates were fulfilled using a method to generate basidiospores in planta. Isolates were characterized by morphology, DNA sequence analysis, hyphal anastomosis, and somatic hyphal interactions. Phylogenetic analyses and hyphal anastomosis criteria support placement of the isolates in R. solani anastomosis group 3 (AG-3). Tomato foliar blight isolates from NC form a single phylogenetic group with tomato isolates of R. solani AG-3 from Japan and are more closely related to R. solani AG-3 isolates from potato than tobacco. Isolates exhibited both compatible and incompatible hyphal interactions when paired in vitro. To our knowledge, this is the first detailed report of tomato foliar blight caused by R. solani AG-3 in North America. A comprehensive description of the technique employed for producing basidiospores is presented with potential utility for understanding foliar disease etiology in other Rhizoctonia pathosystems.

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.

Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA

A series of multilocus sequence-based nuclear DNA markers was developed to infer the phylogeographical history of the Basidiomycetous fungal pathogen Rhizoctonia solani AG-1 IA infecting rice and soybean worldwide. The strategy was based on sequencing of cloned genomic DNA fragments (previously used as RFLP probes) and subsequent screening of fungal isolates to detect single nucleotide polymorphisms (SNPs). Ten primer pairs were designed based on these sequences, which resulted in PCR amplification of 200-320 bp size products and polymorphic sequences in all markers analyzed. By direct sequencing we identified both homokaryon and heterokaryon (i.e. dikaryon) isolates at each marker. Cloning the PCR products effectively estimated the allelic phase from heterokaryotic isolates. Information content varied among markers from 0.5 to 5.9 mutations per 100 bp. Thus, the former RFLP codominant probes were successfully converted into six distinctively variable sequence-based nuclear DNA markers. Rather than discarding low polymorphism loci, the combination of these distinctively variable anonymous nuclear markers would constitute an asset for the unbiased estimate of the phylogeographical parameters such as population sizes and divergent times, providing a more reliable species history that shaped the current population structure of R. solani AG-1 IA.

Divergence between sympatric rice- and soybean-infecting populations of Rhizoctonia solani anastomosis group-1 IA

Rhizoctonia solani anastomosis group (AG)-1 IA causes soybean foliar blighting (aerial blight) and rice sheath blight diseases. Although taxonomically related within the AG-1 complex, sister populations of R. solani AG-1 IA infecting Poaceae (rice) and Fabaceae (soybean) are genetically distinct based on internal transcribed spacer rDNA. However, there is currently no information available regarding the extent of genetic differentiation and host specialization between rice- and soybean-infecting populations of R. solani AG-1 IA. We used 10 microsatellite loci to compare sympatric R. solani AG-1 IA populations infecting rice and soybeans in Louisiana and one allopatric rice-infecting population from Texas. None of the 154 multilocus genotypes found among the 223 isolates were shared among the three populations. Partitioning of genetic diversity showed significant differentiation among sympatric populations from different host species (Phi(ST) = 0.39 to 0.41). Historical migration patterns between sympatric rice- and soybean-infecting populations from Louisiana were asymmetrical. Rice- and soybean-derived isolates of R. solani AG-1 IA were able to infect both rice and soybean, but were significantly more aggressive on their host of origin, consistent with host specialization. The soybean-infecting population from Louisiana was more clonal than the sympatric rice-infecting population. Most of the loci in the soybean-infecting populations were out of Hardy-Weinberg equilibrium (HWE), but the sympatric rice-infecting population from Louisiana was mainly in HWE. All populations presented evidence for a mixed reproductive system.

Genetic structure of populations of Rhizoctonia solani anastomosis group-1 IA from soybean in Brazil

The Basidiomycete fungus Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen of soybean in Brazil, where the average yield losses have reached 30 to 60% in some states in Northern Brazil. No information is currently available concerning levels of genetic diversity and population structure for this pathogen in Brazil. A total of 232 isolates of R. solani AG1 IA were collected from five soybean fields in the most important soybean production areas in central-western, northern, and northeastern Brazil. These isolates were genotyped using 10 microsatellite loci. Most of the multilocus genotypes (MLGTs) were site-specific, with few MLGTs shared among populations. Significant population subdivision was evident. High levels of admixture were observed for populations from Mato Grosso and Tocantins. After removing admixed genotypes, three out of five field populations (Maranhao, Mato Grosso, and Tocantins), were in Hardy-Weinberg (HW) equilibrium, consistent with sexual recombination. HW and gametic disequilibrium were found for the remaining soybean-infecting populations. The findings of low genotypic diversity, departures from HW equilibrium, gametic disequilibrium, and high degree of population subdivision in these R. solani AG-1 IA populations from Brazil are consistent with predominantly asexual reproduction, short-distance dispersal of vegetative propagules (mycelium or sclerotia), and limited long-distance dispersal, possibly via contaminated seed. None of the soybean-infecting populations showed a reduction in population size (bottleneck effect). We detected asymmetric historical migration among the soybean-infecting populations, which could explain the observed levels of subdivision.