Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex

IntroductionMitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species. MethodsIn this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers. Results and DiscussionCompared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome

Insight into trade‐off between wood decay and parasitism from the genome of a fungal forest pathogen

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/91191/1/j.1469-8137.2012.04128.x.pd

A Genome-Wide Association Study Identifies Genomic Regions for Virulence in the Non-Model Organism Heterobasidion annosum ss

The dense single nucleotide polymorphisms (SNP) panels needed for genome wide association (GWA) studies have hitherto been expensive to establish and use on non-model organisms. To overcome this, we used a next generation sequencing approach to both establish SNPs and to determine genotypes. We conducted a GWA study on a fungal species, analysing the virulence of Heterobasidion annosum s.s., a necrotrophic pathogen, on its hosts Picea abies and Pinus sylvestris. From a set of 33,018 single nucleotide polymorphisms (SNP) in 23 haploid isolates, twelve SNP markers distributed on seven contigs were associated with virulence (P,0.0001). Four of the contigs harbour known virulence genes from other fungal pathogens and the remaining three harbour novel candidate genes. Two contigs link closely to virulence regions recognized previously by QTL mapping in the congeneric hybrid H. irregulare6H. occidentale. Our study demonstrates the efficiency of GWA studies for dissecting important complex traits of small populations of non-model haploid organisms with small genomes

Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex

IntroductionMitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species.MethodsIn this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers.Results and DiscussionCompared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome

Overview of four genomic regions significantly associated with <i>Heterobasidion</i> virulence in spruce and pine.

<p>The upper part of each figure plots the <i>p</i>-values (−log10 scale) for the four traits (up- and downstem combined) to the genomic position (in bp). Abbreviations: PFG, fungal growth in pine sapwood; PLL, lesion length in pine; SFG, fungal growth in spruce sapwood; SLL, lesion length in spruce. The lower part displays linkage disequilibrium (LD) heat maps. The heat map illustrates the LD value <i>r</i>² from white to red where red indicates high <i>r</i>² -values. Significant SNP markers are in red. (A) Contig 4128; (B) Contig 41480; (C) Contig 16590; (D) Contig 9600.</p

Haploid isolates of <i>Heterobasidion annosum</i> s.s. used in the study.

a<p>Single spore isolates from basidiospores or conidiospores.</p>b<p>Collectors: JS – J. Stenlid; KK – K. Korhonen; OH – O. Holdenrieder; PC – P. Capretti; IT – I. Thomsen.</p

Data for the contigs with SNPs associated with virulence.

<p>Data for the contigs with SNPs associated with virulence.</p

Sequence data for the fungal isolates.

a<p>Percent aligned compared with total number of reads.</p>b<p>Coverage on reference sequence, Sä16-4, 90211-2 and W15 combined.</p>c<p>Paired-end sequenced isolates.</p

Overview of <i>p</i>-values (−log10 scale) for SNP associations to <i>Heterobasidion</i> virulence in spruce and pine.

<p>The <i>p</i>-values are plotted against the site number from the SNP extraction. The contigs with significant SNPs are indicated with orange lines. Abbreviations: PFG, fungal growth in pine sapwood; PLL, lesion length in pine; SFG, fungal growth in spruce sapwood; SLL, lesion length in spruce.</p