Pectic isozyme profiles of intersterility groups in Heterobasidion annosum

One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020)

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.

Fast and reliable molecular methods to detect fungal pathogens in woody plants

Plant diseases caused by pathogenic microorganisms represent a serious threat to plant productivity, food security, and natural ecosystems. An effective framework for early warning and rapid response is a crucial element to mitigate or prevent the impacts of biological invasions of plant pathogens. For these reasons, detection tools play an important role in monitoring plant health, surveillance, and quantitative pathogen risk assessment, thus improving best practices to mitigate and prevent microbial threats. The need to reduce the time of diagnosis has prompted plant pathologists to move towards more sensitive and rapid methods such as molecular techniques. Considering prevention to be the best strategy to protect plants from diseases, this review focuses on fast and reliable molecular methods to detect the presence of woody plant pathogens at early stage of disease development before symptoms occur in the host. A harmonized pool of novel technical, methodological, and conceptual solutions is needed to prevent entry and establishment of new diseases in a country and mitigate the impact of both invasive and indigenous organisms to agricultural and forest ecosystem biodiversity and productivity.

Ganoderma australe from southern India

The genetic diversity of Ganoderma australe (Fr.) Pat. from southern India was investigated by using ITS1/2 rDNA. The phylogenetic analysis showed that six isolates clustered into two groups viz. biological species I and II. The four strains of BS I (YER03, MYC5, MYC2 and KE) clustered with G. australe TAI-01 and the two other strains of BS II (KMK3 and K39) were grouped with G. australe TAI-05 from Taiwan. The two strains namely TAI-01 and TAI-05 were described as G. australe intersterile Group 1 and 2 from Taiwan, respectively. The higher level nucleotide divergence among BS I and BS II and the high bootstrapping support clearly represent the presence of two biological species of G. australe in southern India which are genetically isolated.

Inferences on the phylogeography of the fungal pathogen Heterobasidion annosum, including evidence of interspecific horizontal genetic transfer and of human-mediated, long-range dispersal

Fungi in the basidiomycete species complex Heterobasidion annosum are significant root-rot pathogens of conifers throughout the northern hemisphere. We utilize a multilocus phylogenetic approach to examine hypotheses regarding the evolution and divergence of two Heterobasidion taxa associated with pines: the Eurasian H. annosum sensu stricto and the North American H. annosum P intersterility group (ISG). Using DNA sequence information from portions of two nuclear and two mitochondrial loci, we infer phylogenetic relationships via parsimony, Bayesian and median-joining network analysis. Analysis of isolates representative of the entire known geographic range of the two taxa results in monophyletic sister Eurasian and North American lineages, with North America further subdivided into eastern and western clades. Genetically anomalous isolates from the Italian presidential estate of Castelporziano are always part of a North American clade and group with eastern North America, upholding the hypothesis of recent, anthropogenically mediated dispersal. P ISG isolates from Mexico have phylogenetic affinity with both eastern and western North America. Results for an insertion in the mitochondrial rDNA suggest this molecule was obtained from the Heterobasidion S ISG, a taxon sympatric with the P ISG in western North America. These data are compatible with an eastern Eurasian origin of the species, followed by dispersal of two sister taxa into western Eurasia and into eastern North America over a Beringean land bridge, a pattern echoed in the phylogeography of other conifer-associated basidiomycetes.

The evolution of the pheromonal signal system and its potential role for reproductive isolation in heterothallic neurospora

Comparative sequencing studies among a wide range of taxonomic groups, including fungi, provide the overall pattern that reproductive genes evolve more rapidly than other genes, and this divergence is believed to be important in the establishment of reproductive barriers between species. In this study, we investigated the molecular evolution of the pheromone receptor genes pre-1 and pre-2 of strains belonging to 12 and 13 heterothallic taxa, respectively, of the model genus Neurospora. Furthermore, we examined the regulatory pattern of both pheromone precursor and receptor genes during sexual crosses of Neurospora crassa and Neurospora intermedia, for which reinforcement of interspecific reproductive barriers in sympatry previously has been documented. We conclude that the part encoding the C-terminal intracellular domain of pre-1 and pre-2 genes evolves rapidly. Both stochastic and directional processes drive this divergence; both genes contain neutrally evolving codons, and in addition, pre-1 contains codons evolving under positive selection, whereas in pre-2 we found highly variable regions with numerous repeats encoding glycine, threonine, or aspartic acid. In addition, we found regulatory changes of the pheromone and receptor genes during crosses between N. crassa and N. intermedia with different reproductive success. Gene expression levels are higher in the interspecific sympatric crosses with low reproductive success than in their intraspecific and/or allopatric equivalents, both at the stage of initial communication and contact and later at postfertilization stages. Taken together, our data indicate that pheromones and receptors are important key players during reproductive isolation between Neurospora species, and this study provides a general framework for future studies on the role of reproductive proteins for reproductive isolation.

Ecological constraints limit the fitness of fungal hybrids in the Heterobasidion annosum species complex

The ability of two closely related species to maintain species boundaries in spite of retained interfertility between them is a documented driving force of speciation. Experimental evidence to support possible interspecific postzygotic isolation mechanisms for organisms belonging to the kingdom Fungi is still missing. Here we report on the outcome of a series of controlled comparative inoculation experiments of parental wild genotypes and F(1) hybrid genotypes between closely related and interfertile taxa within the Heterobasidion annosum fungal species complex. Results indicated that these fungal hybrids are not genetically unfit but can fare as well as parental genotypes when inoculated on substrates favorable to both parents. However, when placed in substrates favoring one of the parents, hybrids are less competitive than the parental genotypes specialized on that substrate. Furthermore, in some but not all fungus x plant combinations, a clear asymmetry in fitness was observed between hybrids carrying identical nuclear genomes but different cytoplasms. This work provides some of the first experimental evidence of ecologically driven postzygotic reinforcement of isolation between closely related fungal species characterized by marked host specificity. Host specialization is one of the most striking traits of a large number of symbiotic and parasitic fungi; thus, we suggest the ecological mechanism proven here to reinforce isolation among Heterobasidion spp. may be generally valid for host-specialized fungi. The validity of this generalization is supported by the low number of known fungal hybrids and by their distinctive feature of being found in substrates different from those colonized by parental species.

Identification of quantitative trait loci affecting virulence in the basidiomycete Heterobasidion annosum s.l

Identification of virulence factors of phytopathogens is important for the fundamental understanding of infection and disease progress in plants and for the development of control strategies. We have identified quantitative trait loci (QTL) for virulence on 1-year-old Pinus sylvestris and 2-year-old Picea abies seedlings and positioned them on a genetic linkage map of the necrotrophic phytopathogen Heterobasidion annosum sensu lato (s.l.), a major root rot pathogen on conifers. The virulence of 102 progeny isolates was analysed using two measurements: lesion lengths and fungal growth in sapwood from a cambial infection site. We found negative virulence effects of hybridization although this was contradicted on a winter-hardened spruce. On P. abies, both measurements identified several partially overlapping QTLs on linkage group (LG) 15 of significant logarithm of odds (LOD) values ranging from 2.31 to 3.85. On P. sylvestris, the lesion length measurement also identified a QTL (LOD 3.09) on LG 15. Moreover, QTLs on two separate smaller LGs, with peak LOD values of 2.78 and 4.58 were identified for fungal sapwood growth and lesion lengths, respectively. The QTL probably represent loci important for specific as well as general aspects of virulence on P. sylvestris and P. abies.

Conifer root and butt rot caused by Heterobasidion annosum (Fr.) Bref. s.l

SUMMARY The root and butt rot caused by Heterobasidon annosum is one of the most destructive diseases of conifers in the northern temperate regions of the world, particularly in Europe. Economic losses attributable to Heterobasidion infection in Europe are estimated at 800 million euros annually. The fungus has been classified into three separate European intersterile species P (H. annosum), S (H. parviporum) and F (H. abietinum) based on their main host preferences: pine, spruce and fir, respectively. In North America, two intersterile groups are present, P and S/F, but these have not been given scientific names. The ecology of the disease spread has been intensively studied but the genetics, biochemistry and molecular aspects of pathogen virulence have been relatively little examined. Recent advances in transcript profiling, molecular characterization of pathogenicity factors and establishment of DNA-transformation systems have paved the way for future advances in our understanding of this pathosystem.

TAXONOMY

Heterobasidion annosum (Fr.) Bref., H. parviporum Niemelä & Korhonen and H. abietinum Niemelä & Korhonen; kingdom Fungi; class Basidiomycotina; order Aphyllophorales; family Bondarzewiaceae; genus Heterobasidion.

IDENTIFICATION

presence of the fungus fruit bodies, basidiocarps whitish in the margins, upper surface is tan to dark brown, usually irregular shaped, 3.5 (-7) cm thick and up to 40 cm in diameter; pores 5-19, 7-22 and 13-26 mm(2) for the P, F and S groups, respectively. Small brownish non-sporulating postules develop on the outside of infected roots. Asexual spores (conidiospores) are 3.8-6.6 x 2.8-5.0 microm in size. Mating tests are necessary for identification of intersterility groups.

HOST RANGE

The fungus attacks many coniferous tree species. In Europe, particularly trees of the genera Pinus and Juniperus (P), Picea (S), Abies (F) and in North America Pinus (P) and Picea, Tsuga and Abies (S/F). To a lesser extent it causes root rot on some decidous trees (Betula and Quercus). Disease symptoms: symptoms (e.g. exhudation of resin, crown deterioration) due to Heterobasidion root rot in living trees are not particularly characteristic and in most cases cannot be distinguished from those caused by other root pathogens. Heterobasidion annosum s.l. is a white rot fungus. Initial growth in wood causes a stain that varies in colour depending on host tree species. Incipient decay is normally pale yellow and it develops into a light brown decay to become a white pocket rot with black flecks in its advanced stage.

CONTROL

silvicultural methods (e.g. stump removal), chemicals (urea, borates) and biological control agent (Phlebiopsis gigantea, marketed as PG Suspension(R) in the UK, PG IBL(R) in Poland and Rotstop(R) in Fennoscandia) are commonly used approaches for minimizing the disease spread.

Sequence polymorphism and molecular characterization of laccase genes of the conifer pathogen Heterobasidion annosum

The oxidizing enzyme laccase produced by many fungi is generally considered to be active in the biodegradation of lignin, a major plant cell wall component highly resistant to microbial attack. The enzyme is secreted at high levels by the P-type of the highly aggressive pathogen Heterobasidion annosum, but at much lower levels by the S-type which correlated with their varying wood decay capability. To investigate the evolutionary relationship between laccase genes of the different H. annosum types from several geographical regions we have compared the nucleotide sequence of the laccase gene from 32 different isolates of the fungus together with two other Asian isolates (H. araucariae, H. insulare). In addition to nucleotide sequence assessment, we have also cloned, characterized and analysed the partial sequences of the laccase gene from the homokaryotic (FSE-7: S-type; Sä16-4: P-type) and heterokaryotic (Faf-8: F-type) strains of H. annosum. Using degenerate primers, two distinct laccase gene fragments of 1.64 and 2 kb were amplified from the genomic DNA of this fungus. DNA sequence analyses showed that the 1.64 kb laccase fragment in all three H. annosum types shared significant homology (86-96%). But comparative analyses of the 1.64 and 2 kb laccase gene fragment revealed only 48% nucleotide sequence similarity. Using the cDNA sequence information, exon regions were predicted and this revealed that about nine small introns interrupted the genomic DNA. Southern hybridization analysis indicated a single copy of the gene in the homokaryotic S-type (FSE-7) examined but presence of double bands in the homokaryotic and heterokaryotic P-type strains of the fungus suggest the existence of two laccase genes. Northern analyses revealed that the gene is constitutively expressed but appear to be enhanced several fold with the addition of ferulic acid or oxalic acid. Alignments of the nucleotide sequences and phylogenetic analyses are presented allowing estimations of evolutionary relationships to be made. These comparisons indicate that laccase gene of P-type is distinct from other Heterobasidion sequences, including the outgroups H. araucariae and H. insulare, while the relationship between the S- and F-groups could not be resolved. Comparative phylogenetic analyses using predicted amino acid sequence also showed strong similarity to the laccases from other basidiomycetes (Pleurotus ostreatus, Phlebia radiata and Trametes versicolor) but least similar to laccases from ascomycete fungi. In addition, the results of McDonald-Kreitman test for possible evidence of selection based on analyses of two exon regions of the H. annosum laccase gene are presented and discussed.

Molecular markers reveal genetic isolation and phylogeography of the S and F intersterility groups of the wood-decay fungus Heterobasidion annosum

The root-rot fungus Heterobasidion annosum (Fr.) Bref. species complex consists of three intersterility groups (S, F, and P), separated by their host affinity. The phylogenetic relationship of the species complex was studied, with the focus on the S and F groups, by comparing DNA sequences of four nuclear gene fragments: calmodulin, glyceraldehyde 3-phosphate dehydrogenase, heat stress protein 80-1, and elongation factor 1-alpha, and one anonymous locus, from 29 fungal isolates originating from Europe, Asia, and North America. The phylogeny of each separate gene locus as well as the combined dataset consisted of three main clades: European F group isolates, Euroasian S group isolates, and North American S group isolates, suggesting them to be separated into phylogenetic species. The results also support the hypothesis of an early separation between the S and F groups, indicating that their distribution have followed their host tree species for a considerable time period.

Heterobasidion annosum 5.8s ribosomal DNA and internal transcribed spacer sequence: rapid identification of European intersterility groups by ribosomal DNA restriction polymorphism

Using conserved fungal ribosomal gene sequences the internal transcribed spacer (ITS) regions one and two (ITS1, ITS2) and the 5.8s ribosomal RNA gene (rRNA) of Heterobasidion annosum were amplified by the polymerase chain reaction (PCR). The nucleotide sequence was determined in three European intersterility groups (ISG-S, -F and -P). Three sequence variants of the ITS were found in ISG-S isolates. The sequence of the ITS of ISG-F differed by two residues from the major ISG-S sequence variant. The ISG-P sequence differed from ISG-S and ISG-F at 15-16 and 16 residues, respectively. Amplified intergenic spacer elements were informative for ISG fingerprinting following digestion with various 4-cutter restriction endonucleases. All differences in the restriction fragments between the ISGs were because of sequence differences in the ITS regions. The fingerprint patterns of isolates from the same intersterility group but from different European localities were identical. These results show that ribosomal DNA fingerprinting is a rapid technique to identify ISGs in Heterobasidion annosum.