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Fusarium head blight (FHB) is a major fungal disease that contributes to severe economic losses for wheat and barley production in Canada and other parts of the world. Rapid developments in molecul...

15 p.-6 fig.-3 tab., Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen’s genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives., This project was financially supported by Academy of Finland (Grant No. 307580). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. A.T.M., S.C., F.J.R.D. and A.S. were funded by the EnzOx2 (BBI-PPP-2015-2-720297; www.enzox2.eu) EU project, and the GENOBIOREF (BIO2017-86559-R) project of the Spanish Ministry of Economy, Industry and Competitiveness,co-financed by FEDER funds.

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Summary Gene expression levels of pathogenesis-related proteins (PR1, PR3, PR5, PR8 and PR9), cell wall modification genes (PAL and expansin), signal transduction genes (ACC oxidase, AOC, MAPK) and a Myb transcription factor were compared in two Hevea brasiliensis budded clones (RRIM612 and PR107) 5 weeks after wounding and artificial inoculation with the white rot fungus, Rigidoporus microporus. PR3 class I chitinase was upregulated in RRIM612 in response to the pathogen when compared with the wounded control. PR9 class IV peroxidase was highly upregulated in PR107. PR1 and PR8 were expressed more in wounded than in inoculated clones. Genes involved in ethylene and jasmonic acid signalling pathways and phenylalanine ammonia-lyase (PAL) were upregulated almost equally in both clones. The Myb transcription factor was upregulated in RRIM612, while MAPK was upregulated in PR107 when compared to the wounded control. The predicted expansin-like protein was upregulated 40-fold in RRIM612 when compared to the wounded control. The results demonstrate the variability in defence responses in different clones and provide the first set of defence genes expression profiles in the host–pathogen interaction of the white rot disease of rubber trees.

Symbiosis with microbes is crucial for survival and development of wood-inhabiting longhorn beetles (Coleoptera: Cerambycidae). Thus, knowledge of the endemic fungal associates of insects would facilitate risk assessment in cases where a new invasive pest occupies the same ecological niche. However, the diversity of fungi associated with insects remains poorly understood. The aim of this study was to investigate fungi associated with the native large poplar longhorn beetle (Saperda carcharias) and the recently introduced Asian longhorn beetle (Anoplophora glabripennis) infesting hardwood trees in Finland. We studied the cultivable fungal associates obtained from Populus tremula colonised by S. carcharias, and Betula pendula and Salix caprea infested by A. glabripennis, and compared these to the samples collected from intact wood material. This study detected a number of plant pathogenic and saprotrophic fungi, and species with known potential for enzymatic degradation of wood components. Phylogenetic analyses of the most commonly encountered fungi isolated from the longhorn beetles revealed an association with fungi residing in the Cadophora-Mollisia species complex. A commonly encountered fungus was Cadophora spadicis, a recently described fungus associated with wood-decay. In addition, a novel species of Cadophora, for which the name Cadophora margaritata sp. nov. is provided, was isolated from the colonised wood.

Rigidoporus microporus (Polyporales, Basidiomycota) syn. Rigidoporus lignosus is the most destructive root pathogen of rubber plantations distributed in tropical and sub-tropical regions. Our primary objective was to characterize Nigerian isolates from rubber tree and compare them with other West African, Southeast Asian and American isolates. To characterize the 20 isolates from Nigeria, we used sequence data of the nuclear ribosomal DNA ITS and LSU, β-tubulin and translation elongation factor 1-α (tef1) gene sequences. Altogether, 40 isolates of R. microporus were included in the analyses. Isolates from Africa, Asia and South/Central America formed three distinctive clades corresponding to at least three species. No phylogeographic pattern was detected among R. microporus collected from West and Central African rubber plantations suggesting continuous gene flow among these populations. Our molecular phylogenetic analysis suggests the presence of two distinctive species associated with the white rot disease. Phylogenetic analyses placed R. microporus in the Hymenochaetales in the vicinity of Oxyporus. This is the first study to characterize R. microporus isolates from Nigeria through molecular phylogenetic techniques, and also the first to compare isolates from rubber plantations in Africa and Asia.

Boreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types ( P < 0.001) and tree species ( P < 0.001). The distance-based linear models analysis showed that environmental variables were significantly correlated with community structure ( P < 0.04). The availability of soil nutrients (Ca [ P = 0.002], Fe [ P = 0.003], and P [ P = 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil ( P < 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera of Agaricomycotina identified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands.

Saprotrophic wood-decaying abilities of (Polyporales, Basidiomycota) syn. and the structural alterations induced in wood blocks of Muell. Arg were studied. Mass loss of wood blocks was analyzed after 3 and 6 months respectively and the patterns of decay by pathogenic and endophytic isolates of this fungus were investigated using light microscopy. Effects of temperature on growth of the isolates on malt extract agar were also investigated. The isolated from a non- host caused the highest percentage mass loss (27.2% after 6 months), followed by isolates ED310 (21.1%) and M13 (15.7%), both collected from diseased plantations. The isolate initially identified as an endophyte showed very low saprotrophic wood decay capability (4.3% after 6 months). The optimal temperature for growth of the isolates was 30 °C; except for the endophytic isolate which showed highest growth at 25 °C. Wood samples degraded by the isolates showed simultaneous attack of wood cell walls, typical of white rot fungi. Results of the study indicate variability in the wood degrading abilities of the isolates and the potential differences in their physiology are discussed. Our findings further support the need for a taxonomical revision of the genus.Rigidoporus microporusRigidoporus lignosusHevea brasiliensisR. microporusH. brasiliensisH. brasiliensisR. microporusRigidoporus

Molecular pathology of forest trees for a long time lagged behind parallel studies on agricultural crop pathology. Recent technological advances have significantly contributed to the observed progress in this field. The first powerful impulse was provided by the completion of the black cottonwood genome sequence in 2006. Genomes of several other important tree species will be completed within a short time. Simultaneously, application of transcriptomics and next-generation sequencing (NGS) has resulted in the rapid accumulation of a vast amount of data on molecular interactions between trees and their microbial parasites. This review provides an overview of our current knowledge about these responses of forest trees to their pathogens, highlighting the achievements of the past decade, discussing the current state of the field, and emphasizing the prospects and challenges for the near future.

Mushroom resources have been exploited in most developed economies because of their huge agro-industrial, medicinal and commercial benefits. Nigerians utilized mushroom-forming fungi only for food and folk medicine for many decades. Auricularia auricular Judae (Bull.) Quel, Lentinus squarrosulus Mont., Pleurotus tuberregium (Fr.) Singer and Volvariella volvacea (Bull.) Singer was some of the common edible mushrooms that were successfully cultivated in Nigeria on small-scale basis. The mushroom resources in Nigeria are grossly under-studied and their attractive potentials under-exploited for addressing economic and industrial development. Resourceful biotechnological approach in the application of mushrooms in agriculture, medicine, industry and environment is inchoate and uncommon in the country.

Background The basidiomycete Rigidoporus microporus is a fungus that causes the white rot disease of the tropical rubber tree, Hevea brasiliensis, the major source of commercial natural rubber. Besides its lifestyle as a pathogen, the fungus is known to switch to saprotrophic growth on wood with the ability to degrade both lignin and cellulose. There is almost no genomic or transcriptomic information on the saprotrophic abilities of this fungus. In this study, we present the fungal transcriptomic profiles during saprotrophic growth on rubber wood. Results A total of 266.6 million RNA-Seq reads were generated from six libraries of the fungus growing either on rubber wood or without wood. De novo assembly produced 34, 518 unigenes with an average length of 2179 bp. Annotation of unigenes using public databases; GenBank, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups (COG) and Gene Ontology (GO) produced 25, 880 annotated unigenes. Transcriptomic profiling analysis revealed that the fungus expressed over 300 genes encoding lignocellulolytic enzymes. Among these, 175 genes were up-regulated in rubber wood. These include three members of the glycoside hydrolase family 43, as well as various glycosyl transferases, carbohydrate esterases and polysaccharide lyases. A large number of oxidoreductases which includes nine manganese peroxidases were also significantly up-regulated in rubber wood. Several genes involved in fatty acid metabolism and degradation as well as natural rubber degradation were expressed in the transcriptome. Four genes (acyl-CoA synthetase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and acyl-CoA acetyltransferase) potentially involved in rubber latex degradation pathway were also induced. A number of ATP binding cassette (ABC) transporters and hydrophobin genes were significantly expressed in the transcriptome during saprotrophic growth. Some genes related to energy metabolism were also induced. Conclusions The analysed data gives an insight into the activation of lignocellulose breakdown machinery of R. microporus. This study also revealed genes with relevance in antibiotic metabolism (e.g. cephalosporin esterase) as well as those with potential applications in fatty acid degradation. This is the first study on the transcriptomic analysis of R. microporus on rubber wood and should serve as a pioneering resource for future studies of the fungus at the genomic or transcriptomic level. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2574-9) contains supplementary material, which is available to authorized users.