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- Dalman, Kerstin, et al.
(författare)
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A genome-wide association study identifies genomic regions for virulence in Heterobasidion annosum s.s
- 2012
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Heterobasidion annosum (Fr.) Bref. sensu lato (s.l.) is a necrotrophic pathogen that causessevere damage to coniferous forests in the Northern Hemisphere. A genome-wide association studyanalysing the virulence of H. annosum sensu stricto (s.s.) on spruce (Picea abies) and pine (Pinussylvestris) using 23 homokaryotic haploid isolates was performed. The virulence of the isolates wasmeasured as lesion length in the phloem and fungal growth within the sapwood followinginoculations in the stem of 2-year-old pine and spruce seedlings. The fungal isolates were sequencedto between 2.6× and 12.6× coverage using the Illumina Genome Analyzer. This data set yielded33,018 single nucleotide polymorphisms (SNPs), with a minor allelic frequency of at least two out of23. These loci were present in all isolates. SNPs and mean values for each virulence trait were usedfor the association study. Twelve SNP markers distributed on seven contigs were found to besignificantly associated with fungal virulence (P< 0.0001). These regions were characterized forlinkage disequilibrium (LD) and gene contents. The LD blocks in these regions ranged between 1.2and 31.2 kb when present. Nine genes encoding calcineurin, acetylglutamate kinase/synthase,cytochrome P450 monooxygenase, serine carboxypeptidase, quinone oxidoreductase (ToxD), twoflavin-containing monooxygenases, exopolyphosphatase and a Swi5 transcription factor wereidentified as candidates for virulence.
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| 2. |
- Dalman, Kerstin, et al.
(författare)
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A Genome-Wide Association Study Identifies Genomic Regions for Virulence in the Non-Model Organism Heterobasidion annosum ss
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Himmelstrand, Kajsa, et al.
(författare)
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Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes
- 2014
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Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 60, s. 303-313
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Tidskriftsartikel (refereegranskat)abstract
- Sizes of mitochondrial genomes vary extensively between fungal species although they typically contain a conserved set of core genes. We have characterised the mitochondrial genome of the conifer root rot pathogen Heterobasidion irregulare and compared the size, gene content and structure of 20 Basidiomycete mitochondrial genomes. The mitochondrial genome of H. irregulare was 114, 193 bp and contained a core set of 15 protein coding genes, two rRNA genes and 26 tRNA genes. In addition, we found six non-conserved open reading frames (ORFs) and four putative plasmid genes clustered in three separate regions together with 24 introns and 14 intronic homing endonuclease genes, unequally spread across seven of the core genes. The size differences among the 20 Basidiomycetes can largely be explained by length variation of intergenic regions and introns. The Agaricomycetes contained the nine largest mitochondrial genomes in the Basidiomycete group and Agaricomycete genomes are significantly (p < 0.001) larger than the other Basidiomycetes. A feature of the Agaricomycete mitochondrial genomes in this study was the simultaneous occurrence of putative plasmid genes and non-conserved ORFs, with Cantharellus cibarius as only exception, where no non-conserved ORF was identified. This indicates a mitochondrial plasmid origin of the non-conserved ORFs or increased mitochondrial genome dynamics of species harbouring mitochondrial plasmids. We hypothesise that two independent factors are the driving forces for large mitochondrial genomes: the homing endonuclease genes in introns and integration of plasmid DNA.
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