Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14

Wibberg, Daniel; Jelonek, Lukas; Rupp, Oliver; Hennig, Magdalena; Eikmeyer, Felix Gregor; Goesmann, Alexander; Hartmann, Anton; Borriss, Rainer; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

doi:10.1016/j.jbiotec.2012.12.010

Cited by 86 publications

(75 citation statements)

References 63 publications

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“…Our comparative analysis indicates that the 203,051 bp long S. borealis mt genome is the second largest fungal mt genome sequenced to date, after the 235,849 bp long mtDNA of the basidiomycete R. solani Rhs1AP [7]. The next largest mitochondrial genomes are the R. solani AG1-IB (162,751 bp) [50] and A. bisporus (135,005 bp) [35]. Expansion of the mitochondrial genome size in R. solani Rhs1AP was driven by accumulation of introns, HEG-like genes and hypothetical genes, but the most peculiar feature was the presence of various interspersed repeats, which occupy about one third of the genome [7].…”

Section: Resultsmentioning

confidence: 88%

The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications

et al. 2014

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Here we report the complete sequence of the mitochondrial (mt) genome of the necrotrophic phytopathogenic fungus Sclerotinia borealis, a member of the order Helotiales of Ascomycetes. The 203,051 bp long mtDNA of S. borealis represents one of the largest sequenced fungal mt genomes. The large size is mostly determined by the presence of mobile genetic elements, which include 61 introns. Introns contain a total of 125,394 bp, are scattered throughout the genome, and are found in 12 protein-coding genes and in the ribosomal RNA genes. Most introns contain complete or truncated ORFs that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Integrations of mobile elements are also evidenced by the presence of two regions similar to fragments of inverton-like plasmids. Although duplications of some short genome regions, resulting in the appearance of truncated extra copies of genes, did occur, we found no evidences of extensive accumulation of repeat sequences accounting for mitochondrial genome size expansion in some other fungi. Comparisons of mtDNA of S. borealis with other members of the order Helotiales reveal considerable gene order conservation and a dynamic pattern of intron acquisition and loss during evolution. Our data are consistent with the hypothesis that horizontal DNA transfer has played a significant role in the evolution and size expansion of the S. borealis mt genome.

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Section: Resultsmentioning

confidence: 88%

The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications

et al. 2014

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“…The large fungal mitochondrial genomes, alike P. radiata mtDNA, expand over 100 kb in size and may include over 50 protein-coding ORFs (Table 5). The tendency for larger fungal mt genomes (over 90 kbp) in the Basidiomycota subphylum Agaricomycotina is pinpointed by recent reports on Moniliopthora perniciosa and M. roreri [24], [28], T. cingulata (over 90 kb) [26], A. bisporus (135 kbp) [23] and R. solani (165 kbp/235 kbp) [50]. This tendency is furthermore confirmed by our study on the 156 kbp P. radiata mtDNA showing up to 126 predicted protein-coding ORFs and 30 RNA genes, which are the second highest numbers reported for the fungal mitochondrial genomes.…”

Section: Discussionmentioning

confidence: 96%

“…12 kb kbp of the Cryptomycota parasite species Rozella allomycis [19] to over 235 kbp (165 kbp main mtDNA [50]) of the Basidiomycota Agaricomycotina species Rhizoctonia solani strain AG3 Rhs1AP (Table 5). Evidence of large variations in the genome size and a high degree of mtDNA structural complexity between eukaryotic organism lineages and species is currently accumulating through sequencing projects.…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial Genome of Phlebia radiata Is the Second Largest (156 kbp) among Fungi and Features Signs of Genome Flexibility and Recent Recombination Events

et al. 2014

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Mitochondria are eukaryotic organelles supporting individual life-style via generation of proton motive force and cellular energy, and indispensable metabolic pathways. As part of genome sequencing of the white rot Basidiomycota species Phlebia radiata, we first assembled its mitochondrial genome (mtDNA). So far, the 156 348 bp mtDNA is the second largest described for fungi, and of considerable size among eukaryotes. The P. radiata mtDNA assembled as single circular dsDNA molecule containing genes for the large and small ribosomal RNAs, 28 transfer RNAs, and over 100 open reading frames encoding the 14 fungal conserved protein subunits of the mitochondrial complexes I, III, IV, and V. Two genes (atp6 and tRNA-IleGAU) were duplicated within 6.1 kbp inverted region, which is a unique feature of the genome. The large mtDNA size, however, is explained by the dominance of intronic and intergenic regions (sum 80% of mtDNA sequence). The intergenic DNA stretches harness short (≤200 nt) repetitive, dispersed and overlapping sequence elements in abundance. Long self-splicing introns of types I and II interrupt eleven of the conserved genes (cox1,2,3; cob; nad1,2,4,4L,5; rnl; rns). The introns embrace a total of 57 homing endonucleases with LAGLIDADGD and GYI-YIG core motifs, which makes P. radiata mtDNA to one of the largest known reservoirs of intron-homing endonucleases. The inverted duplication, intergenic stretches, and intronic features are indications of dynamics and genetic flexibility of the mtDNA, not fully recognized to this extent in fungal mitochondrial genomes previously, thus giving new insights for the evolution of organelle genomes in eukaryotes.

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“…The most comprehensive whole-genome study to date has been that of the rice pathogen AG1-IA [26] [GenBank: AFRT00000000]. The genome assembly of the closely related AG1-IB was published recently [27] [GenBank: CAOJ00000000], however full scaffold sequences were not in the public domain at the time of writing and thus AG1-IB data has not been used for synteny comparisons in this study. The mitochondrial genome sequence of the potato pathogen AG3 strain Rhs1AP and its comparison to that of AG1-IB has been published recently [28].…”

Section: Introductionmentioning

confidence: 99%

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

et al. 2014

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Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA. We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens.

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Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14

Cited by 86 publications

References 63 publications

The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications

The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications

Mitochondrial Genome of Phlebia radiata Is the Second Largest (156 kbp) among Fungi and Features Signs of Genome Flexibility and Recent Recombination Events

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

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