المؤلفون: Chen, Hongxin, Kovalchuk, Andriy, Keriö, Susanna, Asiegbu, Fred O.

المصدر: Mycologia, 2013 Nov 01. 105(6), 1479-1488.

الوصول الحر: https://www.jstor.org/stable/43923716Test

المؤلفون: Mgbeahuruike, Anthony C., Kovalchuk, Andriy, Asiegbu, Fred O.

المصدر: Mycologia, 2013 Nov 01. 105(6), 1471-1478.

الوصول الحر: https://www.jstor.org/stable/43923715Test

المؤلفون: Kovalchuk, Andriy, Lee, Yong-Hwan, Asiegbu, Fred O.

المصدر: Mycologia, 2013 Nov 01. 105(6), 1456-1470.

الوصول الحر: https://www.jstor.org/stable/43923714Test

المؤلفون: Raffaello, Tommaso, Chen, Hongxin, Kohler, Annegret, Asiegbu, Fred O.

المساهمون: Department of Forest Sciences [Helsinki], Faculty of Agriculture and Forestry [Helsinki], University of Helsinki-University of Helsinki, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Academy of Finland, University of Helsinki, Viikki Doctoral Programme in Molecular Biosciences (VGSB), Helsinki Graduate Program in Biotechnology and Molecular Biology (GPBM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)

المصدر: Environmental Microbiology
Environmental Microbiology, Wiley-Blackwell, 2014, 16 (6), pp.1654-1667. ⟨10.1111/1462-2920.12321⟩
Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2014, 16 (6), pp.1654-1667. ⟨10.1111/1462-2920.12321⟩

مصطلحات موضوعية: Basidiomycota, Gene Expression Profiling, [SDV]Life Sciences [q-bio], Pinus sylvestris, Adaptation, Physiological, Wood, complex mixtures, Fungal Proteins, Stress, Physiological, Gene Expression Regulation, Fungal, Plant Bark, Cluster Analysis, Transcriptome, Ecosystem

الوصف: The success of many wood decaying fungi lies in their ability to overcome unfavourable environmental conditions within and outside of litter and wood debris. Although so much has been learned about the ecology, taxonomy and physiology of several wood decaying basidiomycete fungi, the molecular basis for their survival in a diverse range of substrates and ecological habitats has been very little studied. Using the wood decay fungus (Heterobasidion annosum s.s.) as a model, we investigated its transcriptomic response when exposed to several environmental stressors (high and low temperature, osmotic stress, oxidative stress and nutrient starvation) and during growth on specific pine wood compartments (bark, sapwood and heartwood). Among other genes and pathways, we documented the specific induction of the major facilitator superfamily 1 and cytochrome P450 families at low temperature, and protein kinases together with transcription factors during starvation. On the other hand, during saprotrophic growth, we observed the induction of many glycosyl hydrolases, three multi-copper oxidases (MCO), five manganese peroxidases (MnP) and one oxidoreductase which are specific for wood degradation. This is the first study providing insights on the potential mechanisms for adaptation to abiotic stresses and pine heartwood degradation in H. annosum s.s.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::0bf91cb601b5ddb08f02ecc4dffed251Test
https://hal.archives-ouvertes.fr/hal-01268770Test

المؤلفون: Chen, Hongxin, Kovalchuk, Andriy, Keriö, Susanna, Asiegbu, Fred O.

مصطلحات موضوعية: Ascomycota, phylogenetic analysis, Dikarya, cerato-platanin, distribution, Basidiomycota

الوصف: The cerato-platanin family is a group of small cysteine-rich fungal proteins new to science. They usually are abundantly secreted extracellularly and are involved in fungus-host interactions. With the advance of available fungal genome sequences, we performed a genomewide study of the distribution of this family in fungi and analyzed the common characteristics of the protein sequences. A total of 55 fungal genomes, including 27 from Ascomycota and 28 from Basidiomycota, were used. A total of 130 cerato-platanin homolog protein sequences were obtained and analyzed. Our results showed that cerato-platanin homologs existed in both Ascomycota and Basidiomycota but were lost in early branches of jelly fungi as well as in some groups with yeast or yeast-like forms in their life cycle. Homolog numbers varied considerably between Ascomycota and Basidiomycota. Phylogenetic analysis suggested that the ancestor of the Dikarya possessed multiple copies of cerato-platanins, which sorted differently in Ascomycota and Basidiomycota, and that this gene family might have expanded in the Basidiomycota. Almost all homologs contained signal peptide sequences, and the length of mature proteins were mainly 105-134 amino acids. Four cysteines involved in forming two disulfide bridges and signature sequences (CSD or CSN) were highly conserved in most homologs. These results indicated a higher diversity of the cerato-platanin family in Basidiomycota than Ascomycota. ; FIGURE. 1. Distribution of cerato-platanin homologs in Dikarya.Distribution of cerato-platanin homologs in Dikarya.All cerato-platanin mature proteinsFASTA file of all cerato-platanin mature proteinsAll cerato-platanin mature proteins alignments for phylogenetic analysisFASTA files of all the alignments used for both phylogenetic analysesFIGURE. 2. Neighbor-joining phylogenetic tree of cerato-platanin family proteins from Dikarya.Neighbor-joining phylogenetic tree of cerato-platanin family proteins from Dikarya.FIGURE. 3. Maximum likelihood phylogenetic tree of ...

العلاقة: https://zenodo.org/communities/dryadTest; https://zenodo.org/record/5005908Test; https://doi.org/10.5061/dryad.g12k7Test; oai:zenodo.org:5005908

الإتاحة: https://doi.org/10.5061/dryad.g12k7Test
https://doi.org/10.3852/13-115Test
https://zenodo.org/record/5005908Test

المؤلفون: Hongxin Chen, Kovalchuk, Andriy, Keriö, Susanna, Asiegbu, Fred O.

المصدر: Mycologia; Nov/Dec2013, Vol. 105 Issue 6, p1479-1488, 10p

مصطلحات موضوعية: FUNGAL protein genetics, FUNGAL protein analysis, AMINO acid sequence, BASIDIOMYCOTA, ASCOMYCETES

مستخلص: The cerato-platanin family is a group of small cysteine-rich fungal proteins new to science. They usually are abundantly secreted extracellularly and are involved in fungus-host interactions. With the advance of available fungal genome sequences, we performed a genomewide study of the distribution of this family in fungi and analyzed the common characteristics of the protein sequences. A total of 55 fungal genomes, including 27 from Ascomycota and 28 from Basidiomycota, were used. A total of 130 cerato-platanin homolog protein sequences were obtained and analyzed. Our results showed that cerato-platanin homologs existed in both Ascomycota and Basidiomycota but were lost in early branches of jelly fungi as well as in some groups with yeast or yeastlike forms in their life cycle. Homolog numbers varied considerably between Ascomycota and Basidiomycota. Phylogenetic analysis suggested that the ancestor of the Dikarya possessed multiple copies of ceratoplatanins, which sorted differently in Ascomycota and Basidiomycota, and that this gene family might have expanded in the Basidiomycota. Almost all homologs contained signal peptide sequences, and the length of mature proteins were mainly 105-134 amino acids. Four cysteines involved in forming two disulfide bridges and signature sequences (CSD or CSN) were highly conserved in most homologs. These results indicated a higher diversity of the ceratoplatanin family in Basidiomycota than Ascomycota. [ABSTRACT FROM AUTHOR]

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المؤلفون: Oghenekaro, Abbot O.¹ abbot.oghenekaro@helsinki.fi, Miettinen, Otto^2,3, Omorusi, Victor I.⁴, Evueh, Grace A.⁴, Farid, Mohd. A.⁵, Gazis, Romina³, Asiegbu, Fred O.¹

المصدر: Fungal Biology. May2014, Vol. 118 Issue 5/6, p495-506. 12p.

مصطلحات موضوعية: *MOLECULAR phylogeny, *RIGIDOPORUS, *HEVEA, *WHITE rot (Grapes), *POLYPORALES, *BASIDIOMYCOTA, *RUBBER plantations

مستخلص: Abstract: 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. [Copyright &y& Elsevier]

المؤلفون: Sébastien Duplessis, Zhen Zeng, Tommaso Raffaello, Fred O. Asiegbu, Emmanuelle Morin, Eeva J. Vainio, Hui Sun, Andriy Kovalchuk

المساهمون: Department of Forest Sciences [Helsinki], Faculty of Agriculture and Forestry [Helsinki], University of Helsinki-University of Helsinki, Collaborat Innovat Ctr Sustainable Forestry South, Nanjing Forestry University (NFU), Natural Resources Institute Finland, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Academy of Finland research grant 276862, doctoral program in sustainable use of renewable natural resources (AGFOREE) at the University of Helsinki, Department of Forest Sciences, Frederick Asiegbu / Principal Investigator, Viikki Plant Science Centre (ViPS), Helsinki Institute of Sustainability Science (HELSUS), Forest Ecology and Management, Asiegbu, Fred O., Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)

المصدر: BMC Genomics
BMC Genomics, Vol 19, Iss 1, Pp 1-21 (2018)
BMC Genomics, BioMed Central, 2018, 19 (1), ⟨10.1186/s12864-018-4610-4⟩
BMC Genomics 1 (19), . (2018)

مصطلحات موضوعية: 0301 basic medicine, [SDV]Life Sciences [q-bio], INDUCED POINT MUTATIONS, Genome, ANNOTATION, virulence factor, CpG-biased mutation, norvège, Copy-number variation, TRANSCRIPTION FACTOR, 1183 Plant biology, microbiology, virology, 2. Zero hunger, Genetics, 4112 Forestry, biology, Virulence factors, Genomics, facteur de virulence, épinette, Heterobasidion, picea abies, Biotechnology, Research Article, lcsh:QH426-470, lcsh:Biotechnology, Virulence, Genome, Viral, Polymorphism, Single Nucleotide, Heterobasidion parviporum, 03 medical and health sciences, pathogène fongique, lcsh:TP248.13-248.65, Saprotrophic wood decay, Transcription factors, Oxidation-reduction process, Picea, Gene, Plant Diseases, Comparative genomics, europe du nord, LTR RETROTRANSPOSONS, hétérobasidion, Secreted proteins, Basidiomycota, north Europe, LEPTOSPHAERIA-MACULANS, 15. Life on land, biology.organism_classification, DNA-SEQUENCES, NATURAL-SELECTION, lcsh:Genetics, 030104 developmental biology, FUNGAL GENOMES, TRANSPOSABLE ELEMENTS, EVOLUTIONARY ANALYSIS, Reference genome

الوصف: Background Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the pathogenesis and virulence of this species remain elusive. No reference genome to facilitate functional analysis is available for this species. Results To better understand the virulence factor at both phenotypic and genomic level, we characterized 15 H. parviporum isolates originating from different locations across Finland for virulence, vegetative growth, sporulation and saprotrophic wood decay. Wood decay capability and latitude of fungal origins exerted interactive effects on their virulence and appeared important for H. parviporum virulence. We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. Genome-wide alignments and intrinsic polymorphism analysis showed that these isolates exhibited overall high genomic similarity with an average of at least 96% nucleotide identity when compared to the reference, yet had remarkable intra-specific level of polymorphism with a bias for CpG to TpG mutations. Reads mapping coverage analysis enabled the classification of all predicted genes into five groups and uncovered two genomic regions exclusively present in the reference with putative contribution to its higher virulence. Genes enriched for copy number variations (deletions and duplications) and nucleotide polymorphism were involved in oxidation-reduction processes and encoding domains relevant to transcription factors. Some secreted protein coding genes based on the genome-wide selection pressure, or the presence of variants were proposed as potential virulence candidates. Conclusion Our study reported on the first reference genome sequence for this Norway spruce pathogen (H. parviporum). Comparative genomics analysis gave insight into the overall genomic variation among this fungal species and also facilitated the identification of several secreted protein coding genes as putative virulence factors for the further functional analysis. We also analyzed and identified phenotypic traits potentially linked to its virulence. Electronic supplementary material The online version of this article (10.1186/s12864-018-4610-4) contains supplementary material, which is available to authorized users.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9a85a1c57743e83054e967d1e3926e08Test
https://pubmed.ncbi.nlm.nih.gov/29580224Test