A region of heterogeneity adjacent to the 5s ribosomal RNA gene of cereal rusts

IGS Minisatellites Useful for Race Differentiation in Colletotrichum lentis and a Likely Site of Small RNA Synthesis Affecting Pathogenicity

Colletotrichum lentis is a fungal pathogen of lentil in Canada but rarely reported elsewhere. Two races, Ct0 and Ct1, have been identified using differential lines. Our objective was to develop a PCR-probe differentiating these races. Sequences of the translation elongation factor 1α (tef1α), RNA polymerase II subunit B2 (rpb2), ATP citrate lyase subunit A (acla), and internal transcribed spacer (ITS) regions were monomorphic, while the intergenic spacer (IGS) region showed length polymorphisms at two minisatellites of 23 and 39 nucleotides (nt). A PCR-probe (39F/R) amplifying the 39 nt minisatellite was developed which subsequently revealed 1-5 minisatellites with 1-12 repeats in C. lentis. The probe differentiated race Ct1 isolates having 7, 9 or 7+9 repeats from race Ct0 having primarily 2 or 4 repeats, occasionally 5, 6, or 8, but never 7 or 9 repeats. These isolates were collected between 1991 and 1999. In a 2012 survey isolates with 2 and 4 repeats increased from 34% to 67%, while isolated with 7 or 9 repeats decreased from 40 to 4%, likely because Ct1 resistant lentil varieties had been grown. The 39 nt repeat was identified in C. gloeosporioides, C. trifolii, Ascochyta lentis, Sclerotinia sclerotiorum and Botrytis cinerea. Thus, the 39F/R PCR probe is not species specific, but can differentiate isolates based on repeat number. The 23 nt minisatellite in C. lentis exists as three length variants with ten sequence variations differentiating race Ct0 having 14 or 19 repeats from race Ct1 having 17 repeats, except for one isolate. RNA-translation of 23 nt repeats forms hairpins and has the appropriate length to suggest that IGS could be a site of small RNA synthesis, a hypothesis that warrants further investigation. Small RNA from fungal plant pathogens able to silence genes either in the host or pathogen thereby aiding infection have been reported.

Discovery of multiple IGS haplotypes within genotypes of Puccinia striiformis

In a search for specific molecular markers for population analysis of Puccinia striiformis f. sp. tritici, the ribosomal DNA (rDNA) intergenic spacer (IGS) 1 region (rDNA-IGS1, between the 28S and the 5S rDNA genes) was amplified, cloned, and sequenced. It was found to exhibit multiple bands and length polymorphism. Surprisingly, single isolates were found to possess between three to five different IGS1 haplotypes. Bands were cloned and sequenced, and two highly variable regions (α and β) were found between conserved regions, with repeat units interspersed in both types of regions. There were 14 different repeat units, and these were sometimes grouped further into four combinations of repeat units, with a few individual nucleotides (A or C) inserted between the repeats. Among three geographically dispersed isolates, the variable region α was divided into eight types, and the variable region β was divided into two types based on repeat units. Most of the 14 repeat units were shared by the variable and the conserved regions. Among the three isolates, there were a total of 12 IGS1 haplotypes, but some of these were shared between isolates such that there were only eight unique haplotypes. The occurrence of multiple haplotypes within single isolates may be useful for analyzing the population structure, tracking the origin of annual epidemics and providing insights into evolutionary biology of this pathogen.

Fungi vectored by the introduced bark beetle Tomicus piniperda in Ontario, Canada, and comments on the taxonomy of Leptographium lundbergii, Leptographium terebrantis, Leptographium truncatum, and Leptographium wingfieldii

Fungi isolated from Tomicus piniperda (L.) galleries in infected trap logs, standing trees, and directly from insects were identified using morphological features and molecular data obtained from the mitochondrial and nuclear DNA region. Identified strains represented Leptographium wingfieldii Morelet, Leptographium procerum (Kendr.) Wingf., Leptographium lundbergii Lag. & Melin sensu Jacobs & Wingfield, Ophiostoma ips (Rumb.) Nannf., Ophiostoma minus (Hedg.) H. & P. Syd., and Sphaeropsis sapinea sensu lato. Leptographium wingfieldii is believed to be a potentially pathogenic introduced fungus, but sequence data suggest a possible connection between it and the teleomorph of Ophiostoma aureum (Robinson-Jeffrey & Davids.) T.C. Harrington (reported from British Columbia and the western United States). Our data also show that the ex-type culture of Leptographium terebrantis Barras & Perry, a species very similar morphologically to L. wingfieldii, also grouped with L. wingfieldii. We also identified strains of Leptographium truncatum (Wingf. & Marasas) Wingf.; this species has been synonymized with L. lundbergii, but our data indicate that these are distinct species, and therefore, the name L. truncatum should be reinstated. We also report the extended presence of L. procerum in Ontario. Previously viewed as a “southern” species frequently associated with pine-root decline diseases, it has been infrequently reported from New York state and but once each from Ontario and Quebec.

Identification of Ganoderma, the causal agent of basal stem rot disease in oil palm using a molecular method

From comparison of the alignments of the internally transcribed spacers (ITS) of ribosomal DNA from Ganoderma associated with oil palm basal stem rot (BSR) and other Ganoderma species, two specific primer pairs were selected to provide a specific DNA amplification of pathogenic Ganoderma in oil palm. Each primer pair produced a single PCR product of about 450 bp (for primer pair IT1-IT2) and 334 bp (for primer pair IT1-IT3) when oil palm Ganoderma DNA was used. No PCR amplification product was observed when other Ganoderma species DNA was used in PCR amplification with these primer pairs. Three specific restriction enzyme sites were identified in the ITS and intergenic spacer (IGS1) regions. The restriction enzymes MluI, SacI and HinfI were used to digest the ITS-PCR product and restriction enzymes TfiI, ScaI and HincII were used to digest the IGS1-PCR product. Of the three restriction enzymes used in each rDNA region, MluI specifically digested the ITS regions, and TfiI specifically digested the IGS1 region of oil palm Ganoderma. Analysis of the published ITS nucleotide sequences of 31 Ganoderma species showed that the MluI restriction site was not present in other Ganoderma species. The use of both specific primers and restriction enzyme analysis can be applied as a standard protocol to identify pathogenic Ganoderma in oil palm. In this study, the use of specific primers and PCR-RFLP analyses of the rDNA gave consistent results for the characterisation of pathogenic Ganoderma, and indicated that Ganoderma strains associated with BSR disease in oil palms belong to a single species.

Genetic Structure of Heterobasidion annosum in White Fir Mortality Centers in California

ABSTRACT The structure of Heterobasidion annosum populations was studied in 15 mixed-conifer sites in central and northern California. Study sites displayed mortality of white fir trees in enlarging discrete patches (mortality centers). At each site, fungal genotypes were defined by somatic compatibility tests. In two sites, further genetic and molecular analyses were performed on field genotypes and on homokaryons obtained by dedikaryotization of field heterokaryons. Isolates were found to be colonizing mostly the roots and the bole sapwood of white fir trees, and no significant infections of other tree species were observed. Each mortality center was characterized by the presence of several fungal genotypes, all belonging to the S intersterility group. Both homokaryotic and heterokaryotic strains were present in all sites. Multiple genotypes were retrieved in individual trees or stumps. Out of 228 fungal genotypes, 86% were found only within a single tree or stump, while 14% had spread to adjacent trees. The two largest genotypes had diameters of 9 and 10 m, and had colonized five and nine trees, stumps, or both, respectively. The maximum distance between two adjacent trees colonized by the same genotype was 6 m, and a highly significant correlation was found between tree diameter and distance of fungal "vegetative" spread. The largest clones were found in areas characterized by high tree and stump densities, and secondary spread of the fungus was more significant in denser stands. In most cases, original infection courts of existing genotypes could be traced to standing trees and not to stumps. The genetic analysis performed in two mortality centers revealed that most local genotypes had different mating alleles, and thus originated from unrelated basidiospores. In a few cases, the same mating allele was shared by two heterokaryons (n+n genome) or by a homokaryon (n genome) and a heterokaryon. Molecular analysis showed that nuclei bearing the same mating allele were identical, providing evidence that the two nuclei forming heterokaryons can act independently in the field and can be shared among isolates, presumably via di-mon mating or by separate matings of different portions of widespread homokaryons.

RFLP analysis of rRNA intergenic spacer regions of 23 isolates of the entomopathogenPaecilomyces farinosus

Genetic relationships between 23 eastern Canadian isolates of the entomopathogen Paecilomyces farinosus (Holm ex S.F. Gray) Brown & Smith were investigated by comparison of DNA fragments produced by restriction enzyme digestion of polymerase chain reaction amplified ribosomal RNA intergenic spacer regions. The variation observed was limited to 40% or less of these regions. All P. farinosus isolates were very dissimilar to isolates of the entomopathogens Beauveria bassiana (Bals.) Vuill. and Paecilomyces fumosoroseus (Wize) Brown & Smith. Seventeen P. farinosus isolates from six different hosts and diverse habitats yielded identical or nearly identical results. Two groups, each with three isolates from two different hosts, were distinct from the main group of isolates. Each of the three P. farinosus groups included some isolates that produced synnemata and some that did not, indicating multiple evolutionary losses of the ability to produce this sporulation structure. We conclude that eastern Canadian P. farinosus, while genetically and phenotypically variable, is not composed largely of strains with strict ecological requirements. Key words: entomopathogenic fungus, population biology, RFLP, ribosomal RNA intergenic spacer.

Polymorphic restriction patterns of ribosomal internal transcribed spacers in the biocontrol fungus Puccinia carduorum correlate with weed host origin

The internal transcribed spacer (ITS) regions of ribosomal DNA were amplified by PCR and used to develop genetic markers for isolates of Puccinia carduorum being evaluated for biological control of Carduus thoermeri (musk thistle). Unique patterns were produced upon restriction of ITS DNA amplified from four separate Puccinia spp. Restriction patterns of ITS DNA of isolates of P. carduorum from Carduus acanthoides and C. thoermeri were distinct from those of P. carduorum from Carduus tenuiflorus and Carduus pycnocephalus. By this technique, isolates of P. carduorum from four different weed hosts can be differentiated from other Puccinia spp. and separated into two host groups.

Heterogeneity in intergenic regions of the ribosomal repeat of the pine-blister rusts Cronartium flaccidum and Peridermium pini

Mixed aeciospore isolates of Cronartium flaccidum and Peridermium pini were obtained from single-tree infections in Britain, Italy and Greece. The 5.8s ribosomal RNA gene and flanking intergenic transcribed spacer regions ITS1 and ITS2 were found to be highly similar between C. flaccidum and P. pini. Within samples heterogeneity was detected at three nucleotide loci in the ITS1 and at four loci in the ITS2 suggesting that several fungal genotypes may occur at a single infection court. The heterogeneity was confirmed by heteroduplex polymorphism analysis of mixed aeciospore products. RFLP of the ribosomal intergenic spacer region 1 (IGS1) amplified from the same templates indicated limited sequence polymorphism in some copies of this repeated locus. Both the sexual and asexual forms of C. flaccidum show evidence of sequence polymorphism in two independent, non-coding regions of the ribosomal gene array. Variation appears to be greater in the sexual form C. flaccidum, than in the monoaecious form P. pini.

BB. Genetics ofCronartium ribicola. II. Variation in the ribosomal gene cluster

The ribosomal gene repeat in Cronartium ribicola J.C. Fisch is highly variable among spore samples from British Columbia, Canada. Both restriction site variation and length variation occur. Length heterogeneity results from differences in the number of subrepeats in the intergenic spacer (IGS). The number of IGS size classes in haploid cultures is limited but is very large and highly variable in aeciospores from single cankers. The proportions of different size classes vary among cankers on different trees, and among subsamples taken around the periphery of large old cankers. The results are consistent with the fungus having a haploid infective mycelium that produces functional pycnia that result in localized dikaryotic areas following fusion between flexuous hyphae and pycnia. Restriction site variation appears lower than has been reported in range-wide samples of endemic fungal species, consistent with the hypothesis that introduction of C. ribicola to western North America was limited and does not represent the full genetic range of the species. No particular restriction site variants or IGS size classes characterize samples from particular geographic areas. No evidence for geographic races of the fungus was obtained. Keywords: rusts, rust races, ribosomal DNA, intergenic spacer, population structure, RFLP.