Restriction fragment length polymorphisms in mitochondrial DNA and ribosomal RNA gene complexes as an aid to the characterization of species and sub-species populations in the genusVerticillium

"Cryptic" group-I introns in the nuclear SSU-rRNA gene of Verticillium dahliae

Group-I introns are widespread--though irregularly distributed--in eukaryotic organisms, and they have been extensively used for discrimination and phylogenetic analyses. Within the Verticillium genus, which comprises important phytopathogenic fungi, a group-I intron was previously identified in the SSU-rRNA (18S) gene of only V. longisporum. In this work, we aimed at elucidating the SSU-located intron distribution in V. dahliae and other Verticillium species, and the assessment of heterogeneity regarding intron content among rDNA repeats of fungal strains. Using conserved PCR primers for the amplification of the SSU gene, a structurally similar novel intron (sub-group IC1) was detected in only a few V. dahliae isolates. However, when intron-specific primers were used for the screening of a diverse collection of Verticillium isolates that originally failed to produce intron-containing SSU amplicons, most were found to contain one or both intron types, at variable rDNA repeat numbers. This marked heterogeneity was confirmed with qRT-PCR by testing rDNA copy numbers (varying from 39 to 70 copies per haploid genome) and intron copy ratios in selected isolates. Our results demonstrate that (a) IC1 group-I introns are not specific to V. longisporum within the Verticillium genus, (b) V. dahliae isolates of vegetative compatibility groups (VCGs) 4A and 6, which bear the novel intron at most of their rDNA repeats, are closely related, and (c) there is considerable intra-genomic heterogeneity for the presence or absence of introns among the ribosomal repeats. These findings underline that distributions of introns in the highly heterogeneous repetitive rDNA complex should always be verified with sensitive methods to avoid misleading conclusions for the phylogeny of fungi and other organisms.

Structural and phylogenetic analysis of the rDNA intergenic spacer region of Verticillium dahliae

The nuclear ribosomal intergenic spacer (IGS) region was structurally analyzed and exploited for molecular discrimination and phylogenetic analysis of vegetative compatibility groups (VCGs) of Verticillium dahliae. A structural study of 201 available IGS sequences of the fungus was performed, and four classes of ubiquitous repetitive elements, organized in higher-order repetitive structures or composite blocks, were detected in a variable IGS subregion. This subregion was amplified from an international collection of 59 V. dahliae isolates covering all VCGs, together with nine representative V. albo-atrum and V. longisporum isolates, and sequenced. Structural and phylogenetic analyses of the sequences of this polymorphic IGS subregion were consistently informative and allowed the identification of two main lineages in V. dahliae, that is, clade I including VCGs 1A, 1B, 2A, 4B, and 3 and clade II containing VCGs 2B, 4A, and 6. Analysis of IGS sequences proved a highly suitable molecular tool for (a) rapid interspecific differentiation, (b) intraspecific discrimination among VCGs of V. dahliae, facilitating high-throughput VCG confirmation and prediction/profiling, and (c) phylogenetic analysis within and among V. dahliae VCGs.

A phylogenetic analysis of Greek isolates of Aspergillus species based on morphology and nuclear and mitochondrial gene sequences

Aspergillus species originating from Greece were examined by morphological and molecular criteria to explore the diversity of this genus. The phylogenetic relationships of these species were determined using sequences from the ITS and IGS region of the nuclear rRNA gene complex, two nuclear genes ( β -tubulin (benA) and RNA polymerase II second largest subunit (rpb2)) and two mitochondrial genes (small rRNA subunit (rns) and cytochrome oxidase subunit I (cox1)) and, where available, related sequences from databases. The morphological characters of the anamorphs and teleomorphs, and the single gene phylogenetic trees, differentiated and placed the species examined in the well-supported sections of Aenei, Aspergillus, Bispori, Candidi, Circumdati, Clavati, Cremei, Flavi, Flavipedes, Fumigati, Nidulantes, Nigri, Restricti, Terrei, Usti, and Zonati, with few uncertainties. The combined use of the three commonly employed nuclear genes (benA, rpb2, and ITS), the IGS region, and two less often used mitochondrial gene sequences (rns and cox1) as a single unit resolved several taxonomic ambiguities. A phylogenetic tree was inferred using Neighbour-Joining, Maximum Parsimony, and Bayesian methods. The strains examined formed seven well-supported clades within the genus Aspergillus. Altogether, the concatenated nuclear and mitochondrial sequences offer additional tools for an improved understanding of phylogenetic relationships within this genus.

Complete mitochondrial genome of compactin-producing fungus Penicillium solitum and comparative analysis of Trichocomaceae mitochondrial genomes

We determined the complete mitochondrial genome sequence of the compactin-producing fungus Penicillium solitum strain 20-01. The 28 601-base pair circular-mapping DNA molecule encodes a characteristic set of mitochondrial proteins and RNA genes and is intron-free. All 46 protein- and RNA-encoding genes are located on one strand and apparently transcribed in one direction. Comparative analysis of this mtDNA and previously sequenced but unannotated mitochondrial genomes of several medically and industrially important species of the Aspergillus/Penicillium group revealed their extensive similarity in terms of size, gene content and sequence, which is also reflected in the almost perfect conservation of mitochondrial gene order in Penicillium and Aspergillus. Phylogenetic analysis based on concatenated mitochondrial protein sequences confirmed the monophyletic origin of Eurotiomycetes.

Analysis of Verticillium dahliae Suggests a Lack of Correlation Between Genotypic Diversity and Virulence Phenotypes

Verticillium dahliae causes severe wilt and recurring losses in numerous agricultural and ornamental hosts worldwide. Two virulence phenotypes (races) have been identified based on the Ve resistance gene and its homologs but their distribution and evolutionary history are unknown. Sequence analyses of the intergenic spacer of the ribosomal DNA and amplified fragment length polymorphism markers suggested an absence of correlation between genotypic diversity and virulence phenotypes. Additionally, both race 1 and 2 phenotypes were isolated in various geographic regions and hosts. Sustained levels of migration of both virulence phenotypes among various geographic regions were evident, and the study also suggested that both virulence phenotypes infect a variety of hosts, regardless of the availability of resistant cultivars. Given the high genotypic diversity observed in V. dahliae, more than the two known virulence phenotypes may be present in nature but not yet identified because of the current lack of sources of resistance other than the Ve gene and its homologs. The inclusion of various genotypes exhibiting the same virulence phenotype may greatly improve the long-term effectiveness of resistance to race 2 of V. dahliae regardless of the host. This study also confirms the transcontinental gene flow and high genotypic diversity of V. dahliae affecting lettuce in coastal California regardless of the molecular markers employed.

Phylogenetic and biogeographic implications inferred by mitochondrial intergenic region analyses and ITS1-5.8S-ITS2 of the entomopathogenic fungi Beauveria bassiana and B. brongniartii

BACKGROUND

The entomopathogenic fungi of the genus Beauveria are cosmopolitan with a variety of different insect hosts. The two most important species, B. bassiana and B. brongniartii, have already been used as biological control agents of pests in agriculture and as models for the study of insect host - pathogen interactions. Mitochondrial (mt) genomes, due to their properties to evolve faster than the nuclear DNA, to contain introns and mobile elements and to exhibit extended polymorphisms, are ideal tools to examine genetic diversity within fungal populations and genetically identify a species or a particular isolate. Moreover, mt intergenic region can provide valuable phylogenetic information to study the biogeography of the fungus.

RESULTS

The complete mt genomes of B. bassiana (32,263 bp) and B. brongniartii (33,920 bp) were fully analysed. Apart from a typical gene content and organization, the Beauveria mt genomes contained several introns and had longer intergenic regions when compared with their close relatives. The phylogenetic diversity of a population of 84 Beauveria strains -mainly B. bassiana (n = 76) - isolated from temperate, sub-tropical and tropical habitats was examined by analyzing the nucleotide sequences of two mt intergenic regions (atp6-rns and nad3-atp9) and the nuclear ITS1-5.8S-ITS2 domain. Mt sequences allowed better differentiation of strains than the ITS region. Based on mt and the concatenated dataset of all genes, the B. bassiana strains were placed into two main clades: (a) the B. bassiana s. l. and (b) the "pseudobassiana". The combination of molecular phylogeny with criteria of geographic and climatic origin showed for the first time in entomopathogenic fungi, that the B. bassiana s. l. can be subdivided into seven clusters with common climate characteristics.

CONCLUSIONS

This study indicates that mt genomes and in particular intergenic regions provide molecular phylogeny tools that combined with criteria of geographic and climatic origin can subdivide the B. bassiana s.l. entomopathogenic fungi into seven clusters with common climate characteristics.

Detection of pathogenic Verticillium spp. using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Verticillium spp. have been listed by the European and Mediterranean Plant Protection Organization (EPPO) and China as plant quarantine pests. Although attempts have been made to develop a simple routine laboratory assay to detect these organisms, none are routinely used. We describe for the first time a robust assay for reliable identification of Verticillium spp. using protein fingerprinting data obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry(MALDI-TOF-MS). Several sample preparation methods and matrices were investigated to improve mass spectra for the routine identification of six species of Verticillium spp.(Verticillium dahiliae, V. alboatrum, V. fungicola, V. nigrescens, and V. lecanii) by MALDI-TOF-MS. Using the optimized experimental method, we constructed a protein fingerprint database for six species of Verticillium and established a analysis criteria of log(Score). This MALDI-TOF-MS protocol should prove useful as a rapid and reliable assay for distinguishing different Verticillium spp.

Mitochondrial gene sequences alone or combined with ITS region sequences provide firm molecular criteria for the classification of Lecanicillium species

The recent revision of Verticillium sect. Prostrata led to the introduction of the genus Lecanicillium, which comprises the majority of the entomopathogenic strains. Sixty-five strains previously classified as Verticillium lecanii or Verticillium sp. from different geographical regions and hosts were examined and their phylogenetic relationships were determined using sequences from three mitochondrial (mt) genes [the small rRNA subunit (rns), the NADH dehydrogenase subunits 1 (nad1) and 3 (nad3)] and the ITS region. In general, single gene phylogenetic trees differentiated and placed the strains examined in well-supported (by BS analysis) groups of L. lecanii, L. longisporum, L. muscarium, and L. nodulosum, although in some cases a few uncertainties still remained. nad1 was the most informative single gene in phylogenetic analyses and was also found to contain group I introns with putative open reading frames (ORFs) encoding for GIY-YIG endonucleases. The combined use of mt gene sequences resolved taxonomic uncertainties arisen from ITS analysis and, alone or in combination with ITS sequences, helped in placing uncharacterised Verticillium lecanii and Verticillium sp. firmly into Lecanicillium species. Combined gene data from all the mt genes and all the mt genes and the ITS region together, were very similar. Furthermore, a relaxed correlation with host specificity -- at least for Homoptera -- was indicated for the rns and the combined mt gene sequences. Thus, the usefulness of mt gene sequences as a convenient molecular tool in phylogenetic studies of entomopathogenic fungi was demonstrated.

Molecular characterization of isolates of Beauveria bassiana obtained from overwintering and summer populations of Sunn Pest (Eurygaster integriceps)

AIM

To examine whether isolates of the entomopathogenic fungus Beauveria bassiana are more closely associated to their summer hosts compared with overwintering hosts, with recently developed molecular tools based on mitochondrial regions.

METHODS AND RESULTS

Primers for the traditional ITS1-5.8S-ITS2 region and two mitochondrial intergenic regions, namely, nad3-atp9 and atp6-rns, were used. All amplified products were sequenced, aligned and Neighbour-Joining (NJ), parsimony and Bayesian phylogenetic inference analyses were performed. The isolates examined were grouped with very good support into three distinct groups, two of them showed geographical correlation, but no clear association to their host.

CONCLUSIONS

The mitochondrial intergenic regions used were more informative than the nuclear ITS1-5.8S-ITS2 sequences. The sequence variability observed, that allowed the phylogenetic placement of the isolates into distinct groups, depended on the geographical origin of the isolates and can be exploited for designing group-specific and isolate-specific primers for their genetic fingerprinting. No clear associations with summer Sunn Pest populations were observed.

SIGNIFICANCE AND IMPACT OF THE STUDY

Studies on the genetic variability of biocontrol agents like B. bassiana are indispensable for the development of molecular tools for their future monitoring.

The complete mitochondrial genome of the vascular wilt fungus Verticillium dahliae: a novel gene order for Verticillium and a diagnostic tool for species identification

The complete sequence (27,184 bp) of the mitochondrial (mt) genome of the phytopathogenic fungus Verticillium dahliae has been determined. It contains 14 protein-coding genes related to oxidative phosphorylation, two rRNA genes and a set of 25 tRNA genes. A single intron, that harbors an intronic ORF coding for a putative ribosomal protein (rps), is located within the large rRNA gene (rnl). Gene order comparisons of V. dahliae mtDNA and complete mt genomes of Pezizomycotina revealed four units of synteny for Sordariomycetes, namely rnl-trn ((11-12))-nad2-nad3, nad4L-nad5-cob-cox1, nad1-nad4-atp8-atp6 and rns-trn ((1-5))-cox3-trn ((1-5))-nad6-trn ((2-5)). These four units, in different combinations, merged to single continuous unit in the orders of Hypocreales and Sordariales. V. dahliae (Phyllachorales) and all members of the genus showed a unique feature which is the translocation of the nad1-nad4-atp8-atp6-rns-cox3-nad6 region in between genes nad3 and atp9 of the Hypocreales mtDNA gene order. Analysis of mt intergenic sequences of Verticillium species permitted the design of a species-specific primer allowing the discrimination of V. longisporum against V. dahliae and V. albo-atrum. By considering the protein-coding gene sequences as one unit, a phylogenetic comparison with representatives of Ascomycota complete mtDNA was performed.

The complete mitochondrial genome of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae: gene order and trn gene clusters reveal a common evolutionary course for all Sordariomycetes, while intergenic regions show variation

The mitochondrial genome (mtDNA) of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae, with a total size of 24,673 bp, was one of the smallest known mtDNAs of Pezizomycotina. It contained the 14 typical genes coding for proteins related to oxidative phosphorylation, the two rRNA genes, a single intron that harbored an intronic ORF coding for a putative ribosomal protein (rps) within the large rRNA gene (rnl), and a set of 24 tRNA genes which recognized codons for all amino acids, except proline and valine. Gene order comparison with all known mtDNAs of Sordariomycetes illustrated a highly conserved genome organization for all the protein- and rRNA-coding genes, as well as three clusters of tRNA genes. By considering all mitochondrial essential protein-coding genes as one unit a phylogenetic study of these small genomes strongly supported the common evolutionary course of Sordariomycetes (100% bootstrap support) and highlighted the advantages of analyzing small genomes (mtDNA) over single genes. In addition, comparative analysis of three intergenic regions demonstrated sequence variability that can be exploited for intra- and inter-specific identification of Metarhizium.

Molecular and immunochemical phylogeny of Verticillium species

21 strains with all typical morphological characteristics of eight Verticillium species (Phyllachorales) were studied in this work, together with representatives from four Hypocreales species (11 strains), that were previously classified as members of the genus. The PCR products from two nuclear genes, i.e. the ITS1-5.8S-ITS2 region and RNA polymerase II largest subunit gene (rpb1), together with four mitochondrial genes, i.e. the small ribosomal rRNA subunit (rns), the two NADH dehydrogenase subunit genes (nad1 and nad3), and the cytochrome oxidase subunit III gene (cox3) were sequenced and analyzed. Similarly, antibodies raised against one strain of each of the species examined (V. nubilum and V. theobromae excluded) were used against the proteins of all other strains. The number and relative area of precipitates formed after crossed electrophoreses served to estimate the degree of immunochemical relatedness. Combined molecular and immunochemical data clarified the phylogenetic relationships of all true Verticillium species and provided a convincing insight into the evolutionary relation of the sect. Nigrescentia with members of the sect. Verticillium and sect. Prostrata that until recently were included in Verticillium.

Electrophoretic karyotype and gene mapping of the vascular wilt fungus Verticillium dahliae

The karyotype profile of Verticillium dahliae was resolved by pulse-field gel electrophoresis. It revealed 6 chromosomal bands that corresponded to 7 chromosomes as shown by RFLP analysis using as probe the telomeric consensus sequence (AACCCT)(5). The number of chromosomes was further verified by the sensitivity of the hybridization signals to Bal31 digestion and the exclusion of interfering mitochondrial DNA signals. The corresponding sizes of the seven separated chromosomes were 6.7, 5.6, 4.1, 3.4, 3.1, 3.1 and 2.4Mb, raising the total genomic size of the fungus to approximately 28.4Mb. Twenty five homologous V. dahliae genes obtained either from randomly sequenced clones or PCR amplification were used as hybridization probes and were located onto the seven chromosomes.

The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications

The mitochondrial genome (mtDNA) of the entomopathogenic fungus Lecanicillium muscarium (synonym Verticillium lecanii) with a total size of 24,499-bp has been analyzed. So far, it is the smallest known mitochondrial genome among Pezizomycotina, with an extremely compact gene organization and only one group-I intron in its large ribosomal RNA (rnl) gene. It contains the 14 typical genes coding for proteins related to oxidative phosphorylation, the two rRNA genes, one intronic ORF coding for a possible ribosomal protein (rps), and a set of 25 tRNA genes which recognize codons for all amino acids, except alanine and cysteine. All genes are transcribed from the same DNA strand. Gene order comparison with all available complete fungal mtDNAs-representatives of all four Phyla are included-revealed some characteristic common features like uninterrupted gene pairs, overlapping genes, and extremely variable intergenic regions, that can all be exploited for the study of fungal mitochondrial genomes. Moreover, a minimum common mtDNA gene order could be detected, in two units, for all known Sordariomycetes namely nad1-nad4-atp8-atp6 and rns-cox3-rnl, which can be extended in Hypocreales, to nad4L-nad5-cob-cox1-nad1-nad4-atp8-atp6 and rns-cox3-rnl nad2-nad3, respectively. Phylogenetic analysis of all fungal mtDNA essential protein-coding genes as one unit, clearly demonstrated the superiority of small genome (mtDNA) over single gene comparisons.

Molecular characterization of Aphanomyces species associated with legumes

The identification of plant-associated isolates of Aphanomyces spp. has been mainly based on morphological characters. These types of features, however, can be unreliable due to their high variation and degree of overlap between different taxa. In this work, strains of Aphanomyces, with plant pathogenic and non-pathogenic characteristics, derived mainly from the roots of several leguminous crops in Sweden, as well as a number of reference strains of A. euteiches, A. cladogamus and A. cochlioides were compared by morphology, AT-rich DNA RFLPs and sequence analysis of the total ITS/5.8S rRNA gene region. Parsimony analysis of the sequence data of the total ITS region of 21 strains separated the taxa at the specific level, while two intra-specific groups were also detected within A. euteiches. One comprised all pathogenic isolates of A. euteiches from Sweden, together with two isolates from France and the USA. These isolates formed a homogenous group with identical ITS regions and a single AT-rich DNA RFLP banding pattern. The second ITS subspecific group included reference strains of A. euteiches with preferential pathogenicity to bean and alfalfa, all of which originated from the USA. The bean and alfalfa pathotypes were further distinguished by their different AT-rich DNA RFLPs. The non-pathogenic isolates of Aphanomyces from Sweden associated with the roots of several legumes, formed a genotypically uniform group with an identical ITS sequence and a single AT-rich DNA RFLP pattern. The ITS sequence of this group was identical to that of reference strains of A. cladogamus, suggesting that the non-pathogenic isolates belonged to this species. Intra-specific AT-rich DNA banding profiles were also obtained for isolates of A. cladogamus and these patterns corresponded well to the original hosts.

Characterization of Verticillium albo-atrum Field Isolates Using Pathogenicity Data and AFLP Analysis

Since 1997, hop wilt induced by a virulent pathotype of Verticillium albo-atrum has caused considerable economic losses in hop fields in Slovenia. In all, 20 isolates of V. albo-atrum, including 12 from plants affected with the lethal form (PG2) of hop wilt, 6 from plants with the mild form (PG1), 1 from cucumber, and 1 from petunia, as well as 1 isolate of V. dahliae each from hop and green pepper, were analyzed by amplified fragment length polymorphism (AFLP). Differences in the virulence of hop isolates were confirmed by pathogenicity tests on hop cultivars. The AFLP method was optimized for analysis of these fungi and 7 of 39 primer combinations tested were used for the analysis of polymorphism among isolates. Cluster analysis of AFLP data divided the isolates into two, well-separated V. albo-atrum and V. dahliae clusters, confirming that the two species are genetically distinct. Within the V. albo-atrum cluster, isolates were further separated into two distinct groups: the A1 group contained PG1 hop pathotype and cucumber and petunia isolates, and the A2 group all hop isolates of the PG2 pathotype. Minor genetic variation was detected within pathotype-associated AFLP groups, but the clear separation of V. albo-atrum hop isolates according to their level of virulence shows genetic differentiation among hop V. albo-atrum pathotypes.

Standard and Swedish variant types of the hybrid alder Phytophthora attacking alder in Hungary

A new Phytophthora disease of common alder (Alnus glutinosa) similar to that previously reported in several countries in Europe has been observed in Hungary. Based on these earlier studies, the alder Phytophthora was considered likely to be a hybrid between P cambivora and a P fragariae-like species: across Europe a range of new alder Phytophthora is spreading that comprise a range of heteroploid hybrids including a 'standard' hybrid type and several other hybrid types termed 'variants'. Phenotypic and molecular features of the pathogen in Hungary were characterised and compared with isolates from elsewhere. The morphologies of five isolates from one region (Hévíz) resembled the common, 'standard' type, whereas the three isolates from another region (Hanság) exhibited traits similar to those of one of the 'variant' types, ie the Swedish 'variant'. Molecular markers of these two groups of Hungarian isolates also represented a good fit to those of the standard type and the Swedish variant, respectively. Isozyme patterns and profiles of restriction fragments of the entire internal transcribed spacer (ITS) region or mitochondrial DNAs and of RAPD-PCR products did not differ within a group, but distinct polymorphisms were exhibited between the two groups of isolates. Southern analysis of random amplified polymorphic DNA (RAPD) revealed the homologous nature of co-migrating bands of P cambivora and the isolates of alder Phytophthora. Furthermore, restriction fragment profiles of the ITS region of ribosomal DNAs and the mtDNAs were consistent with reported biparental origin of alder Phytophthora. The hybrid status of these continuously evolving pathogens raises many issues and challenges concerning efficient control measures.

Genetic, morphological, and virulence characterization of the entomopathogenic fungus Verticillium lecanii

In order to clarify relationships among genetic diversity, virulence, and other characteristics of conidia, 46 isolates of Verticillium lecanii from various hosts and geographical locations were examined. The internal transcribed spacer (ITS) and intergenic spacer (IGS) regions of ribosomal DNA (rDNA), mitochondrial small subunit rDNA (mt-SrDNA) and beta-tubulin were analyzed by PCR-RFLP. PCR-single stranded conformational polymorphism (SSCP) was performed on regions of the mitochondrial large subunit rDNA, mt-SrDNA, beta-tubulin and histone 4. There were no relationships among the results of RFLP, SSCP, isolation source, and location. However, amplified product size of IGS did have relationships with conidia size and sporulation. Six isolates with 4.0-kb IGS products had large conidia dimensions, and yielded low numbers of conidia compared with other isolates. Three out of the six isolates were high virulence (over 90%) against green peach aphids. Furthermore, double-stranded RNA (dsRNA) was detected in 22 out of 35 V. lecanii isolates and related with the amplicon sizes of IGS, though not with virulence or isolation location. Isolates containing dsRNA were divided into six distinct types based on banding pattern. These data demonstrate the level of genetic diversity of V. lecanii, and suggest relations among the genetic properties and conidial morphology.

IGS sequence variation, group-I introns and the complete nuclear ribosomal DNA of the entomopathogenic fungus Metarhizium: excellent tools for isolate detection and phylogenetic analysis

The complete nuclear rDNA gene complex of Metarhizium anisopliae var. anisopliae isolate ME1 is 8118bp long and contains the 18S, 5.8S, and 28S rRNA genes as well as the ITS and IGS regions. Variation in the ITS of isolates of M. anisopliae var. anisopliae and one each of Metarhizium anisopliae var. acridum, Metarhizium flavoviride var. flavoviride, and Metarhizium flavoviride var. minus, clustered 39 out of 40 of M. anisopliae var. anisopliae isolates in one clade. Nucleotide sequence variation in the IGS among 21 of M. anisopliae var. anisopliae isolates showing IGS length variation sorted them into three strongly supported clades, which were weakly correlated with insect hosts and were not correlated with geographic location. Two group-I introns, Ma-int4 and Ma-int5, were discovered in the 18S and the 3(') end of the 28S, in M. anisopliae var. anisopliae isolates ITALY-12 and IMBST 9601. The insertion sites and sub-group of these introns correlated with their closest relatives, as judged by phylogenetic analysis of intron nucleotide sequence.

Restriction analysis of PCR amplified nrDNA regions revealed intraspecific variation within populations of Fusarium culmorum

Seventy-five isolates of Fusarium culmorum with diverse geographical origin and host were analyzed using restriction digestion of polymerase chain reaction amplified nuclear ribosomal DNA intergenic spacer (IGS) and 28S gene regions. The 28S gene was conserved and has produced identical restriction patterns, however, the IGS region was substantially variable. The isolates were divided into 29 unique IGS haplotypes. There was limited resolution between clustering of isolates and their origin and/or host. The variability was distributed largely equally at both macro- and micro-geographical scale. The phylogeographic distribution pattern suggests a seed-borne dispersal of F. culmorum.

Identification of group-I introns at three different positions within the 28S rDNA gene of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae

Using a set of heterologous primers designed from the 3'-end of the 28S rRNA gene of Verticillium dahliae the corresponding gene region of 30 isolates of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae was amplified. The polymerase chain reaction products obtained could be classified into four groups varying in size from 1.0 to 2.2 kb. Sequence analyses of representative PCR products revealed the presence of five distinct introns, positioned in three different insertion sites. Fungal isolates 316 and 11 both harbored one intron each (374 and 337 bp in size, respectively), whereas isolate 33 harbored three introns (436, 334, and 412 bp) within the relevant 28S rRNA region. All five introns shared the conserved P, Q, R, S elements and all the other characteristic features of group-I introns in their deduced secondary structure; three (316-int, 33-int1, and 33-int3) belong to subgroup IC1 and two (33-int2 and 11-int) belong to subgroup IE. Further, reverse transcription polymerase chain reactions indicated that all these introns were absent from the mature RNA molecules. The appearance of the five introns at identical positions with those from other organisms belonging to various phyla is discussed.

The complete DNA sequence of the nuclear ribosomal RNA gene complex of Verticillium dahliae: intraspecific heterogeneity within the intergenic spacer region

The complete DNA sequence of the nuclear ribosomal RNA gene complex of Verticillium dahliae: Intraspecific heterogeneity within the intergenic spacer region. Fungal Genetics and Biology 29, 19-27. The complete sequence of the nuclear ribosomal DNA gene complex of the phytopathogenic fungus Verticillium dahliae has been determined. The tandemly repeated unit was 7216 bp long and appears to be the shortest rDNA cluster described so far among filamentous fungi. Primer pairs were designed for amplification of the region spanning half of the 28S subunit, the intergenic spacer (IGS), and the 5' end of 18S subunit of a number of Verticillium strains, isolated from various hosts and geographic origins. Great heterogeneity was detected in the amplified products of the IGS region resulting in fragments varying from 1.6 to 2.0 kb. The majority of Verticillium isolates were classified into two groups with 1.6- and 1.7-kb amplified products, respectively. The former group included 31 V. dahliae, 7 V. longisporum, and 1 V. albo-atrum isolates, whereas the latter included 10 V. dahliae and 1 V. albo-atrum isolates. Sequence analysis of representative PCR products of the above groups identified a "hot-spot" region harboring most of larger insertions, whereas most of the small changes were due to transitions and transversions. One V. longisporum isolate with a 2.0-kb PCR product contained 13 perfectly conserved tandem repeats of 39 bp long. The presence of similar incomplete sequences in the corresponding regions of V. dahliae, V. longisporum, and V. albo-atrum isolates revealed a particular standard motif of insertions in the IGS region of the genus and is discussed.

Characterization of Populations of Rhizoctonia solani in Paddy Rice Fields in Côte d'Ivoire

ABSTRACT Isolates of Rhizoctonia solani were obtained from plant and soil samples that had been systematically collected in a field experiment in Côte d'Ivoire to study the diversity of the pathogen and the influence of three different rice rotations on the pathogen population. Characterization by morphology, anastomosis testing, pathogenicity testing, and restriction fragment length polymorphisms (RFLPs) of AT-rich DNA (AT-DNA) showed that there were no differences in isolates from different experimental plots, suggesting that the soil as well as the plant population of the fungus was indistinguishable throughout the experiment and was not influenced by crop rotation. Analysis of AT-DNA showed that the isolates obtained from plant material and one from soil shared a distinct banding pattern, identical with the AT-DNA RFLP obtained for the reference strain of anastomosis group 1 (AG-1). The remaining soil isolates produced a consistent RFLP pattern that was distinct from that of the plant isolates. Morphological characterization of isolates produced two major clusters consisting of the same groups of isolates as found by AT-DNA RFLP. Diversity in morphological characters was much higher in plant than in soil isolates and indicated that the population might consist of several clones. Anastomosis testing revealed that soil as well as plant isolates were able to fuse with the tester strain of AG-1. Significant differences in disease severity were observed between the two groups of isolates in pathogenicity tests on rice plants, with plant isolates being distinctively more virulent.

Presence of a 20 bp insertion/deletion in the ITS1 region of Verticillium lecanii

Polymerase chain reaction (PCR) amplification of the complete ribosomal RNA internally transcribed spacer (ITS) region of 36 isolates of Verticillium lecanii and related species gave a single 620 bp product in 31 isolates. Five isolates received as V. lecanii, however, gave a single product of 600 bp. Restriction fragment analysis of the PCR products from all isolates gave consistent patterns for the 31 isolates with a 620 bp product. The five isolates with the 600 bp product showed only minor discrepancies to these, generally related to the size of only one restriction fragment. The total ITS region was sequenced from 10 typical 620 bp isolates and one 600 bp isolate. Sequence variation between the isolates varied from 0 to 14.5%, and the 20 bp size discrepancy was found to relate to an insertion or deletion in the centre of the ITS1 region.

Identification of Molecular Variants in Mitochondrial DNAs of Members of the Genera Beauveria, Verticillium, Paecilomyces, Tolypocladium , and Metarhizium

A set of five mitochondrial (mt) probes derived from a strain of Beauveria bassiana was used to evaluate the similarity of mtDNAs from 15 additional isolates of this fungus and five genera of other entomopathogenic fungi. The probes and genes encoded for (shown in parentheses) were pBbmtE2 ( NADI, ATP6 ), pBbmtE3 ( ATP6 , small rRNA [ srRNA ]), pBbmtE4 ( srRNA, CO3, NAD6 ), pBbSE1 ( NAD6, tRNA Val, Ile, Ser, Trp, Pro , large rRNA [ lrRNA ]), and pBbXS1 ( lrRNA ). The probes produced identical hybridization patterns in Eco RI-digested DNA from nearly all isolates of B. bassiana and Beauveria caledonica . Similar patterns were also observed with Beauveria densa . The isolates of B. caledonica and B. densa DNAs could be differentiated from each other and from B. bassiana on the basis of a Hin dIII digestion and probing with pBbmtE3. Probe pBbmtE2 produced either a 5.0-kb or a 4.1-kb band in all of the B. bassiana isolates. This observation was used to categorize the mtDNA of B. bassiana into two types, designated A and B. Hybridization of the five probes produced distinct banding patterns in Beauveria brongniartii, Tolypocladium cylindrosporum, Tolypocladium nivea, Metarhizium anisopliae, Verticillium lecanii , and Paecilomyces farinosus . Hybridizations carried out with multiple probes simultaneously present produced unique patterns which characterized the B. bassiana group from all other fungi tested. These results are discussed in terms of how mtDNA polymorphisms in B. bassiana may relate to natural population structures, mt transmission in deuteromycetes, and the use of mtDNA polymorphisms in structural analysis of mtDNA.