Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3
Wibberg D, Genzel F, Verwaaijen B, Blom J, Rupp O, Goesmann A, Zrenner R, Grosch R, Pühler A, Schlüter A (2017)
Archives of Microbiology 199(7): 1065-1068.
Zeitschriftenaufsatz
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Autor*in
Wibberg, DanielUniBi;
Genzel, Franziska;
Verwaaijen, BartUniBi;
Blom, Jochen;
Rupp, Oliver;
Goesmann, Alexander;
Zrenner, Rita;
Grosch, Rita;
Pühler, AlfredUniBi 
;
Schlüter, AndreasUniBi
;
Schlüter, AndreasUniBi Abstract / Bemerkung
The basidiomycetes fungus Rhizoctonia solani AG3 is responsible for black scurf disease on potato and occurs in each potato growing area world-wide. In this study, the draft genome sequence of the black scurf pathogen R. solani AG3-PT isolate Ben3 is presented. The genome sequence of R. solani AG3-PT isolate Ben3 consists of 1385 scaffolds. These scaffolds amount to a size of approx. 51 Mb. Considering coverage analyses of contigs, the size of the diploid genome was estimated to correspond to 116 Mb. Gene prediction by applying AUGUSTUS (3.2.1.) resulted in 12,567 identified genes. Based on automatic annotation using GenDBE, genes potentially encoding cellulases and enzymes involved in secondary metabolite synthesis were identified in the R. solani AG3-PT isolate Ben3 genome. Comparative analyses including the R. solani AG3 isolate Rhs1AP, also originating from potato, revealed first insights into core genes shared by both isolates and unique determinants of each isolate.
Stichworte
Ultrafast sequencing;
AUGUSTUS;
GenDBE;
EDGAR
Erscheinungsjahr
2017
Zeitschriftentitel
Archives of Microbiology
Band
199
Ausgabe
7
Seite(n)
1065-1068
ISSN
0302-8933
eISSN
1432-072X
Page URI
https://pub.uni-bielefeld.de/record/2916490
Zitieren
Wibberg D, Genzel F, Verwaaijen B, et al. Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Archives of Microbiology. 2017;199(7):1065-1068.
Wibberg, D., Genzel, F., Verwaaijen, B., Blom, J., Rupp, O., Goesmann, A., Zrenner, R., et al. (2017). Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Archives of Microbiology, 199(7), 1065-1068. doi:10.1007/s00203-017-1394-x
Wibberg, Daniel, Genzel, Franziska, Verwaaijen, Bart, Blom, Jochen, Rupp, Oliver, Goesmann, Alexander, Zrenner, Rita, Grosch, Rita, Pühler, Alfred, and Schlüter, Andreas. 2017. “Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3”. Archives of Microbiology 199 (7): 1065-1068.
Wibberg, D., Genzel, F., Verwaaijen, B., Blom, J., Rupp, O., Goesmann, A., Zrenner, R., Grosch, R., Pühler, A., and Schlüter, A. (2017). Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Archives of Microbiology 199, 1065-1068.
Wibberg, D., et al., 2017. Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Archives of Microbiology, 199(7), p 1065-1068.
D. Wibberg, et al., “Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3”, Archives of Microbiology, vol. 199, 2017, pp. 1065-1068.
Wibberg, D., Genzel, F., Verwaaijen, B., Blom, J., Rupp, O., Goesmann, A., Zrenner, R., Grosch, R., Pühler, A., Schlüter, A.: Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Archives of Microbiology. 199, 1065-1068 (2017).
Wibberg, Daniel, Genzel, Franziska, Verwaaijen, Bart, Blom, Jochen, Rupp, Oliver, Goesmann, Alexander, Zrenner, Rita, Grosch, Rita, Pühler, Alfred, and Schlüter, Andreas. “Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3”. Archives of Microbiology 199.7 (2017): 1065-1068.
1 Zitation in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Biosynthesis of Oxylipins by Rhizoctonia solani with Allene Oxide and Oleate 8S,9S-Diol Synthase Activities.
Oliw EH., Lipids 53(5), 2018
PMID: 30009385
Oliw EH., Lipids 53(5), 2018
PMID: 30009385
32 References
Daten bereitgestellt von Europe PubMed Central.
GJ, Am Potato J 66(), 1989
EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Blom J, Albaum SP, Doppmeier D, Puhler A, Vorholter FJ, Zakrzewski M, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19457249
Blom J, Albaum SP, Doppmeier D, Puhler A, Vorholter FJ, Zakrzewski M, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19457249
EDGAR 2.0: an enhanced software platform for comparative gene content analyses.
Blom J, Kreis J, Spanig S, Juhre T, Bertelli C, Ernst C, Goesmann A., Nucleic Acids Res. 44(W1), 2016
PMID: 27098043
Blom J, Kreis J, Spanig S, Juhre T, Bertelli C, Ernst C, Goesmann A., Nucleic Acids Res. 44(W1), 2016
PMID: 27098043
Anastomosis groups, pathogenicity and sensitivity to fungicides of Rhizoctonia solani isolates collected on potato crops in France.
Campion C, Chatot C, Perraton B, Andrivon D., Eur. J. Plant Pathol. 109(9), 2003
PMID: IND43637029
Campion C, Chatot C, Perraton B, Andrivon D., Eur. J. Plant Pathol. 109(9), 2003
PMID: IND43637029
Hyphal anastomosis reactions, rDNA-internal transcribed spacer sequences, and virulence levels among subsets of Rhizoctonia solani anastomosis group-2 (AG-2) and AG-BI.
Carling DE, Kuninaga S, Brainard KA., Phytopathology 92(1), 2002
PMID: IND23274695
Carling DE, Kuninaga S, Brainard KA., Phytopathology 92(1), 2002
PMID: IND23274695
Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP.
Cubeta MA, Thomas E, Dean RA, Jabaji S, Neate SM, Tavantzis S, Toda T, Vilgalys R, Bharathan N, Fedorova-Abrams N, Pakala SB, Pakala SM, Zafar N, Joardar V, Losada L, Nierman WC., Genome Announc 2(5), 2014
PMID: 25359908
Cubeta MA, Thomas E, Dean RA, Jabaji S, Neate SM, Tavantzis S, Toda T, Vilgalys R, Bharathan N, Fedorova-Abrams N, Pakala SB, Pakala SM, Zafar N, Joardar V, Losada L, Nierman WC., Genome Announc 2(5), 2014
PMID: 25359908
Genetic diversity of Rhizoctonia solani associated with potato tubers in France.
Fiers M, Edel-Hermann V, Heraud C, Gautheron N, Chatot C, Le Hingrat Y, Bouchek-Mechiche K, Steinberg C., Mycologia 103(6), 2011
PMID: 21642342
Fiers M, Edel-Hermann V, Heraud C, Gautheron N, Chatot C, Le Hingrat Y, Bouchek-Mechiche K, Steinberg C., Mycologia 103(6), 2011
PMID: 21642342
Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica.
Gkarmiri K, Finlay RD, Alstrom S, Thomas E, Cubeta MA, Hogberg N., BMC Genomics 16(), 2015
PMID: 26296338
Gkarmiri K, Finlay RD, Alstrom S, Thomas E, Cubeta MA, Hogberg N., BMC Genomics 16(), 2015
PMID: 26296338
Development of a specific PCR assay for the detection of Rhizoctonia solani AG 1-IB using SCAR primers.
Grosch R, Schneider JH, Peth A, Waschke A, Franken P, Kofoet A, Jabaji-Hare SH., J. Appl. Microbiol. 102(3), 2007
PMID: 17309631
Grosch R, Schneider JH, Peth A, Waschke A, Franken P, Kofoet A, Jabaji-Hare SH., J. Appl. Microbiol. 102(3), 2007
PMID: 17309631
GA, Potato Res 37(), 1994
r2cat: synteny plots and comparative assembly.
Husemann P, Stoye J., Bioinformatics 26(4), 2009
PMID: 20015948
Husemann P, Stoye J., Bioinformatics 26(4), 2009
PMID: 20015948
Genomic insights that advance the species definition for prokaryotes.
Konstantinidis KT, Tiedje JM., Proc. Natl. Acad. Sci. U.S.A. 102(7), 2005
PMID: 15701695
Konstantinidis KT, Tiedje JM., Proc. Natl. Acad. Sci. U.S.A. 102(7), 2005
PMID: 15701695
S, J Gen Plant Pathol 66(), 2000
Infection with Rhizoctonia solani Induces Defense Genes and Systemic Resistance in Potato Sprouts Grown Without Light
Lehtonen MJ, Somervuo P, Valkonen JPT., Phytopathology 98(11), 2008
PMID: IND44142548
Lehtonen MJ, Somervuo P, Valkonen JPT., Phytopathology 98(11), 2008
PMID: IND44142548
The carbohydrate-active enzymes database (CAZy) in 2013.
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24270786
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24270786
Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3.
Losada L, Pakala SB, Fedorova ND, Joardar V, Shabalina SA, Hostetler J, Pakala SM, Zafar N, Thomas E, Rodriguez-Carres M, Dean R, Vilgalys R, Nierman WC, Cubeta MA., FEMS Microbiol. Lett. 352(2), 2014
PMID: 24461055
Losada L, Pakala SB, Fedorova ND, Joardar V, Shabalina SA, Hostetler J, Pakala SM, Zafar N, Thomas E, Rodriguez-Carres M, Dean R, Vilgalys R, Nierman WC, Cubeta MA., FEMS Microbiol. Lett. 352(2), 2014
PMID: 24461055
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
A, Annu Rev Phytopathol 25(), 1987
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Puhler A, Noll T, Goesmann A., PLoS ONE 9(1), 2014
PMID: 24427317
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Puhler A, Noll T, Goesmann A., PLoS ONE 9(1), 2014
PMID: 24427317
Classification of Rhizoctonia spp. using rDNA-ITS sequence analysis supports the genetic basis of the classical anastomosis grouping
Sharon M, Kuninaga S, Hyakumachi M, Naito S, Sneh B., Mycoscience 49(2), 2008
PMID: IND44043570
Sharon M, Kuninaga S, Hyakumachi M, Naito S, Sneh B., Mycoscience 49(2), 2008
PMID: IND44043570
AUGUSTUS: ab initio prediction of alternative transcripts.
Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845043
Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845043
WR, 2001
R, Annu Rev Phytopathol 32(), 1994
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH., Nucleic Acids Res. 43(W1), 2015
PMID: 25948579
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH., Nucleic Acids Res. 43(W1), 2015
PMID: 25948579
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, Hennig M, Eikmeyer F, Goesmann A, Hartmann A, Borriss R, Grosch R, Puhler A, Schluter A., J. Biotechnol. 167(2), 2012
PMID: 23280342
Wibberg D, Jelonek L, Rupp O, Hennig M, Eikmeyer F, Goesmann A, Hartmann A, Borriss R, Grosch R, Puhler A, Schluter A., J. Biotechnol. 167(2), 2012
PMID: 23280342
Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates.
Wibberg D, Rupp O, Blom J, Jelonek L, Krober M, Verwaaijen B, Goesmann A, Albaum S, Grosch R, Puhler A, Schluter A., PLoS ONE 10(12), 2015
PMID: 26690577
Wibberg D, Rupp O, Blom J, Jelonek L, Krober M, Verwaaijen B, Goesmann A, Albaum S, Grosch R, Puhler A, Schluter A., PLoS ONE 10(12), 2015
PMID: 26690577
Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system.
Wibberg D, Rupp O, Jelonek L, Krober M, Verwaaijen B, Blom J, Winkler A, Goesmann A, Grosch R, Puhler A, Schluter A., J. Biotechnol. 203(), 2015
PMID: 25801332
Wibberg D, Rupp O, Jelonek L, Krober M, Verwaaijen B, Blom J, Winkler A, Goesmann A, Grosch R, Puhler A, Schluter A., J. Biotechnol. 203(), 2015
PMID: 25801332
Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes.
Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Puhler A, Fogelqvist J, Varrelmann M, Schluter A, Dixelius C., BMC Genomics 17(), 2016
PMID: 26988094
Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Puhler A, Fogelqvist J, Varrelmann M, Schluter A, Dixelius C., BMC Genomics 17(), 2016
PMID: 26988094
Draft genome sequence of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB strain BBA69670.
Wibberg D, Andersson L, Rupp O, Goesmann A, Puhler A, Varrelmann M, Dixelius C, Schluter A., J. Biotechnol. 222(), 2016
PMID: 26851388
Wibberg D, Andersson L, Rupp O, Goesmann A, Puhler A, Varrelmann M, Dixelius C, Schluter A., J. Biotechnol. 222(), 2016
PMID: 26851388
PS, Plant Pathol 57(), 2008
PHI-base: a new database for pathogen host interactions.
Winnenburg R, Baldwin TK, Urban M, Rawlings C, Kohler J, Hammond-Kosack KE., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381911
Winnenburg R, Baldwin TK, Urban M, Rawlings C, Kohler J, Hammond-Kosack KE., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381911
Characterization of Rhizoctonia solani from potato in Great Britain
AUTHOR UNKNOWN, Plant Pathol. 56(2), 2007
PMID: IND43887798
AUTHOR UNKNOWN, Plant Pathol. 56(2), 2007
PMID: IND43887798
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