Characterization of Heterobasidion occidentale transcriptomes reveals candidate genes and DNA polymorphisms for virulence variations

Abstract

SummaryCharacterization of genes involved in differentiation of pathogen species and isolates with variations of virulence traits provides valuable information to control tree diseases for meeting the challenges of sustainable forest health and phytosanitary trade issues. Lack of genetic knowledge and genomic resources hinders novel gene discovery, molecular mechanism studies and development of diagnostic tools in the management of forest pathogens. Here, we report on transcriptome profiling of Heterobasidion occidentale isolates with contrasting virulence levels. Comparative transcriptomic analysis identified orthologous groups exclusive to H. occidentale and its isolates, revealing biological processes involved in the differentiation of isolates. Further bioinformatics analyses identified an H. occidentale secretome, CYPome and other candidate effectors, from which genes with species‐ and isolate‐specific expression were characterized. A large proportion of differentially expressed genes were revealed to have putative activities as cell wall modification enzymes and transcription factors, suggesting their potential roles in virulence and fungal pathogenesis. Next, large numbers of simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were detected, including more than 14 000 interisolate non‐synonymous SNPs. These polymorphic loci and species/isolate‐specific genes may contribute to virulence variations and provide ideal DNA markers for development of diagnostic tools and investigation of genetic diversity.

Transcriptomic Reprogramming and Genetic Variations Contribute to Western Hemlock Defense and Resistance Against Annosus Root and Butt Rot Disease

“…In addition to RNA-seq, genome-wide association analysis (GWAS) was also used to identify the SNPs and the candidate genes significantly associated with Norway spruce susceptibility to H. parviporum ( Mukrimin et al, 2018 ). A previous study characterized a large set of secreted proteins as candidate effectors in the H. occidentale transcriptome ( Liu et al, 2018 ). Effectors from pests/pathogens have capacity to suppress the NLR-dependent host resistance by directly binding to the NLRs or other molecular mechanisms ( Derevnina et al, 2021 ).…”

“…RNA-seq reads were first filtered by Trimmomatic 1 with default setting at Illuminaclip: TruSeq3-PE.fa:2:30:10, Leading: 3, Trailing: 3, Slidingwindow: 4:15, Minlen: 36 ( Bolger et al, 2014 ). To detect H. occidentale genes expressed in Hemlock stem tissues, RNA-seq reads were mapped to a reference transcriptome assembled from RNA-seq reads of H. occidentale mycelium cultures in a previous study ( Liu et al, 2018 ). Mapping was performed using CLC Genomics Workbench (v5.5) with minimum length fraction = 0.9, and minimum similarity fraction = 0.98.…”

The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce

“…They found that HIRHG was up-regulated during infection and maybe important for the pathogen to grow in a pectin containing environment. Liu et al 37 compared the transcriptomes of two different H. occidentale isolates grown on apple fruits. Their results suggest that the capacity of H. occidentale to colonize apple fruit correlated with the expression of potential carbohydrate active enzyme genes 37 .…”

Phenotypic Recovery of a Heterobasidion Isolate Infected by a Debilitation-Associated Virus Is Related to Altered Host Gene Expression and Reduced Virus Titer

“…They are also capable of both necrotic and saprotrophic growth. H. irregulare was the first Heterobasidion species to be characterized for complete genome sequence ( Olson et al, 2012 ; Garbelotto and Gonthier, 2013 ), and thereafter also genomes of H. annosum ( Sillo et al, 2015 ; Choi et al, 2017 ), H. occidentale ( Liu et al, 2018 ), and H. parviporum ( Zeng et al, 2018 ) have been characterized. There are different preventive control methods practiced against these root rot fungi, but truly curative methods are urgently needed.…”