Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

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Zeng , Z , Sun , H , Vainio , E J , Raffaello , T , Kovalchuk , A , Morin , E , Duplessis , S & Asiegbu , F O 2018 , ' Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors ' , BMC Genomics , vol. 19 , 220 . https://doi.org/10.1186/s12864-018-4610-4

Title: Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors
Author: Zeng, Zhen; Sun, Hui; Vainio, Eeva J.; Raffaello, Tommaso; Kovalchuk, Andriy; Morin, Emmanuelle; Duplessis, Sebastien; Asiegbu, Fred O.
Contributor: University of Helsinki, Department of Forest Sciences
University of Helsinki, Department of Forest Sciences
University of Helsinki, Department of Forest Sciences
University of Helsinki, Department of Forest Sciences
University of Helsinki, Department of Forest Sciences
Date: 2018-03-27
Language: eng
Number of pages: 21
Belongs to series: BMC Genomics
ISSN: 1471-2164
URI: http://hdl.handle.net/10138/234615
Abstract: 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.
Subject: Heterobasidion parviporum
Comparative genomics
Virulence factors
Secreted proteins
CpG-biased mutation
Saprotrophic wood decay
Oxidation-reduction process
Transcription factors
INDUCED POINT MUTATIONS
TRANSPOSABLE ELEMENTS
FUNGAL GENOMES
LEPTOSPHAERIA-MACULANS
EVOLUTIONARY ANALYSIS
LTR RETROTRANSPOSONS
TRANSCRIPTION FACTOR
NATURAL-SELECTION
DNA-SEQUENCES
ANNOTATION
1183 Plant biology, microbiology, virology
4112 Forestry
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