Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14
Wibberg D, Jelonek L, Rupp O, Kröber M, Eikmeyer FG, Goesmann A, Hartmann A, Borriss R, Grosch R, Pühler A, Schlüter A (2013)
Journal of Biotechnology 167(2): 142-155.
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Autor*in
Wibberg, DanielUniBi;
Jelonek, LukasUniBi;
Rupp, OliverUniBi;
Kröber, MagdalenaUniBi;
Eikmeyer, Felix GregorUniBi ;
Goesmann, AlexanderUniBi ;
Hartmann, Anton;
Borriss, Rainer;
Grosch, Rita;
Pühler, AlfredUniBi ;
Schlüter, AndreasUniBi
Einrichtung
Abstract / Bemerkung
Anastomosis group AG1-IB isolates of the anamorphic basidiomycetous fungus Rhizoctonia solani Kühn affect various agricultural and horticultural important crops including bean, rice, soybean, figs, hortensia, cabbage and lettuce. To gain insights into the genome structure and content, the first draft genome sequence of R. solani AG1-IB isolate 7/3/14 was established. Four complete runs on the Genome Sequencer (GS) FLX platform (Roche Applied Science) yielding approx. a 25-fold coverage of the R. solani genome were accomplished. Assembly of the sequence reads by means of the gsAssembler software version 2.6 applying the heterozygotic mode resulted in numerous contigs and scaffolds and a predicted size of 87.1Mb for the diploid status of the genome. 'Contig-length vs. read-count' analysis revealed that the assembled contigs can be classified into five different groups. Detailed BLAST-analysis revealed that most contigs of group II feature high-scoring matches to other contigs of the same group suggesting that distinguishable allelic variants exist for many genes. Due to the supposed diploid and heterokaryotic nature of R. solani AG1-IB 7/3/14, this result has been anticipated. However, the heterokaryotic character of the isolate is not really supported by sequencing data obtained for the isolate R. solani AG1-IB 7/3/14. Coverage of group III contigs is twice as high as for group II contigs which can also be explained by the diploid status of the genome and indistinguishable alleles on homologous chromosomes. Assembly of sequence data led to the identification of the rRNA unit (group V contigs) and the mitochondrial (mt) genome (group IV contigs) which is a circular molecule of 162,751bp in size featuring a GC-content of 36.4%. The R. solani 7/3/14 mt-genome is one of the largest fungal mitochondrial genomes known to date. Its large size essentially is due to the presence of numerous non-conserved hypothetical ORFs and introns. Gene prediction for the R. solani AG1-IB 7/3/14 genome was conducted by the Augustus Gene Prediction Software for Eukaryotes (version 2.6.) applying the parameter set for the fungus Coprinopsis cinerea okayama 7#130. Gene prediction and annotation provided first insights into the R. solani AG1-IB 7/3/14 gene structure and content. In total, 12,422 genes were predicted. The average number of exons per gene is five. Exons have a mean length of 214bp, whereas introns on average are 66bp in length. Annotation of the genome revealed that 4169 of 12,422 genes could be assigned to KOG functional categories.
Erscheinungsjahr
2013
Zeitschriftentitel
Journal of Biotechnology
Band
167
Ausgabe
2
Seite(n)
142-155
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/2549908
Zitieren
Wibberg D, Jelonek L, Rupp O, et al. Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. Journal of Biotechnology. 2013;167(2):142-155.
Wibberg, D., Jelonek, L., Rupp, O., Kröber, M., Eikmeyer, F. G., Goesmann, A., Hartmann, A., et al. (2013). Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. Journal of Biotechnology, 167(2), 142-155. doi:10.1016/j.jbiotec.2012.12.010
Wibberg, Daniel, Jelonek, Lukas, Rupp, Oliver, Kröber, Magdalena, Eikmeyer, Felix Gregor, Goesmann, Alexander, Hartmann, Anton, et al. 2013. “Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14”. Journal of Biotechnology 167 (2): 142-155.
Wibberg, D., Jelonek, L., Rupp, O., Kröber, M., Eikmeyer, F. G., Goesmann, A., Hartmann, A., Borriss, R., Grosch, R., Pühler, A., et al. (2013). Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. Journal of Biotechnology 167, 142-155.
Wibberg, D., et al., 2013. Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. Journal of Biotechnology, 167(2), p 142-155.
D. Wibberg, et al., “Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14”, Journal of Biotechnology, vol. 167, 2013, pp. 142-155.
Wibberg, D., Jelonek, L., Rupp, O., Kröber, M., Eikmeyer, F.G., Goesmann, A., Hartmann, A., Borriss, R., Grosch, R., Pühler, A., Schlüter, A.: Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. Journal of Biotechnology. 167, 142-155 (2013).
Wibberg, Daniel, Jelonek, Lukas, Rupp, Oliver, Kröber, Magdalena, Eikmeyer, Felix Gregor, Goesmann, Alexander, Hartmann, Anton, Borriss, Rainer, Grosch, Rita, Pühler, Alfred, and Schlüter, Andreas. “Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14”. Journal of Biotechnology 167.2 (2013): 142-155.
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Eukaryotic peptide chain release factor subunit 1 OS=Podospora anserina GN=SU2 PE=3 SV=1 (UNIPROT: M5BJ27)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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Ribosome biogenesis protein ERB1 (UNIPROT: M5BKP8)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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Inorganic phosphate transport protein PHO88 OS=Saccharomyces cerevisiae (Strain ATCC 204508 / S288c) (UNIPROT: M5BU07)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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Retrotransposon-derived protein PEG10 OS=Mus musculus GN=Peg10 PE=1 SV=2 (UNIPROT: M5CGJ9)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
Download in FASTA format
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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alpha-1,2-Mannosidase (UNIPROT: M5C4X4)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
Download in FASTA format
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
Download in FASTA format
54S ribosomal protein rml2, mitochondrial OS=Schizosaccharomyces pombe (Strain 972 / ATCC 24843) GN= (UNIPROT: M5BUJ4)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
Download in FASTA format
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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Uncharacterized protein (UNIPROT: M5CGG8)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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NFYB protein (UNIPROT: M5C7R1)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
Download in FASTA format
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
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Peptide hydrolase (UNIPROT: M5CFE4)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
Download in FASTA format
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
Download in FASTA format
Putative endo-beta-1,4-glucanase D OS=Aspergillus niger (Strain CBS 513,88 / FGSC A1513) GN=eglD PE= (UNIPROT: M5BRS5)
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
Download in FASTA format
Organism: Thanatephorus cucumeris (strain AG1-IB / isolate 7/3/14)
Download in FASTA format
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