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, Kröber M, Verwaaijen B, Goesmann A, Albaum S, Grosch R, Pühler A, Schlüter A (2015)
Plos One 10(12): e0144769.

Download
OA 724.86 KB
Journal Article | Original Article | Published | English
Abstract
Rhizoctonia solani, a soil-born plant pathogenic basidiomycetous fungus, affects various economically important agricultural and horticultural crops. The draft genome sequence for the R. solani AG1-IB isolate 7/3/14 as well as a corresponding transcriptome dataset (Expressed Sequence Tags-ESTs) were established previously. Development of a specific R. solani AG1-IB gene model based on GMAP transcript mapping within the eukaryotic gene prediction platform AUGUSTUS allowed detection of new genes and provided insights into the gene structure of this fungus. In total, 12,616 genes were recognized in the genome of the AG1-IB isolate. Analysis of predicted genes by means of different bioinformatics tools revealed new genes whose products potentially are involved in degradation of plant cell wall components, melanin formation and synthesis of secondary metabolites. Comparative genome analyses between members of different R. solani anastomosis groups, namely AG1-IA, AG3 and AG8 and the newly annotated R. solani AG1-IB genome were performed within the comparative genomics platform EDGAR. It appeared that only 21 to 28% of all genes encoded in the draft genomes of the different strains were identified as core genes. Based on Average Nucleotide Identity (ANI) and Average Amino-acid Identity (AAI) analyses, considerable sequence differences between isolates representing different anastomosis groups were identified. However, R. solani isolates form a distinct cluster in relation to other fungi of the phylum Basidiomycota. The isolate representing AG1-IB encodes significant more genes featuring predictable functions in secondary metabolite production compared to other completely sequenced R. solani strains. The newly established R. solani AG1-IB 7/3/14 gene layout now provides a reliable basis for post-genomics studies.
Publishing Year
ISSN
Financial disclosure
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
PUB-ID

Cite this

Wibberg D, Rupp O, Blom J, et al. 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. Plos One. 2015;10(12): e0144769.
Wibberg, D., Rupp, O., Blom, J., Jelonek, L., Kröber, M., Verwaaijen, B., Goesmann, A., et al. (2015). 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. Plos One, 10(12), e0144769. doi:10.1371/journal.pone.0144769
Wibberg, D., Rupp, O., Blom, J., Jelonek, L., Kröber, M., Verwaaijen, B., Goesmann, A., Albaum, S., Grosch, R., Pühler, A., et al. (2015). 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. Plos One 10:e0144769.
Wibberg, D., et al., 2015. 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. Plos One, 10(12): e0144769.
D. Wibberg, et al., “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”, Plos One, vol. 10, 2015, : e0144769.
Wibberg, D., Rupp, O., Blom, J., Jelonek, L., Kröber, M., Verwaaijen, B., Goesmann, A., Albaum, S., Grosch, R., Pühler, A., Schlüter, A.: 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. Plos One. 10, : e0144769 (2015).
Wibberg, Daniel, Rupp, Oliver, Blom, Jochen, Jelonek, Lukas, Kröber, Magdalena, Verwaaijen, Bart, Goesmann, Alexander, Albaum, Stefan, Grosch, Rita, Pühler, Alfred, and Schlüter, Andreas. “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”. Plos One 10.12 (2015): e0144769.
Main File(s)
Access Level
OA Open Access
Last Uploaded
2016-11-24T13:33:07Z

This data publication is cited in the following publications:
This publication cites the following data publications:

1 Citation in Europe PMC

Data provided by Europe PubMed Central.

An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH.
Nguyen TV, Wibberg D, Battenberg K, Blom J, Vanden Heuvel B, Berry AM, Kalinowski J, Pawlowski K., BMC Genomics 17(1), 2016
PMID: 27729005

36 References

Data provided by Europe PubMed Central.

The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
AUTHOR UNKNOWN, 2005

AUTHOR UNKNOWN, 0
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
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM., Int. J. Syst. Evol. Microbiol. 57(Pt 1), 2007
PMID: 17220447
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
AUTHOR UNKNOWN, 2008
Cross-kingdom patterns of alternative splicing and splice recognition.
McGuire AM, Pearson MD, Neafsey DE, Galagan JE., Genome Biol. 9(3), 2008
PMID: 18321378
AUGUSTUS: A web server for gene prediction in eukaryotes that allows user-defined constraints
AUTHOR UNKNOWN, 2005
LTR Retrotransposons in Fungi
AUTHOR UNKNOWN, 2011
The role of cutinase in fungal pathogenicity.
Schafer W., Trends Microbiol. 1(2), 1993
PMID: 8044466
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
Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations
AUTHOR UNKNOWN, 2008

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 26690577
PubMed | Europe PMC

Search this title in

Google Scholar