Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors
| العنوان: | Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors |
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| 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) |
| سنة النشر: | 2017 |
| 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 |
| تدمد: | 1471-2164 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9a85a1c57743e83054e967d1e3926e08Test https://pubmed.ncbi.nlm.nih.gov/29580224Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....9a85a1c57743e83054e967d1e3926e08 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14712164 |
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