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Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes

Overview of attention for article published in BMC Genomics, March 2016
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Title
Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes
Published in
BMC Genomics, March 2016
DOI 10.1186/s12864-016-2561-1
Pubmed ID
Authors

Daniel Wibberg, Louise Andersson, Georgios Tzelepis, Oliver Rupp, Jochen Blom, Lukas Jelonek, Alfred Pühler, Johan Fogelqvist, Mark Varrelmann, Andreas Schlüter, Christina Dixelius

Abstract

Sugar beet (Beta vulgaris) is a crop cultivated for its high content in sugar, but it is vulnerable to many soil-borne pathogens. One of them is the basidiomycete Rhizoctonia solani. This fungal species has a compatibility system regulating hyphal fusions (anastomosis). Consequently, R. solani species are categorized in anastomosis groups (AGs). AG2-2IIIB isolates are most aggressive on sugar beet. In the present study, we report on the draft genome of R. solani AG2-2IIIB using the Illumina technology. Genome analysis, interpretation and comparative genomics of five sequenced R. solani isolates were carried out. The draft genome of R. solani AG2-2IIIB has an estimated size of 56.02 Mb. In addition, two normalized EST libraries were sequenced. In total 20,790 of 21,980 AG2-2IIIB isotigs (transcript isoforms) were mapped on the genome with more than 95 % sequence identity. The genome of R. solani AG2-2IIIB was predicted to harbor 11,897 genes and 4908 were found to be isolate-specific. R. solani AG2-2IIIB was predicted to contain 1142 putatively secreted proteins and 473 of them were found to be unique for this isolate. The R. solani AG2-2IIIB genome encodes a high number of carbohydrate active enzymes. The highest numbers were observed for the polysaccharide lyases family 1 (PL-1), glycoside hydrolase family 43 (GH-43) and carbohydrate estarase family 12 (CE-12). Transcription analysis of selected genes representing different enzyme clades revealed a mixed pattern of up- and down-regulation six days after infection on sugar beets featuring variable levels of resistance compared to mycelia of the fungus grown in vitro. The established R. solani AG2-2IIIB genome and EST sequences provide important information on the gene content, gene structure and transcriptional activity for this sugar beet pathogen. The enriched genomic platform provides an important platform to enhance our understanding of R. solani biology.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 86 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
India 1 1%
Unknown 85 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 24 28%
Researcher 20 23%
Student > Master 13 15%
Student > Doctoral Student 6 7%
Student > Bachelor 3 3%
Other 10 12%
Unknown 10 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 46 53%
Biochemistry, Genetics and Molecular Biology 13 15%
Chemistry 4 5%
Computer Science 2 2%
Business, Management and Accounting 1 1%
Other 2 2%
Unknown 18 21%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 21 March 2016.
All research outputs
#15,521,944
of 25,388,229 outputs
Outputs from BMC Genomics
#5,697
of 11,236 outputs
Outputs of similar age
#172,291
of 332,741 outputs
Outputs of similar age from BMC Genomics
#123
of 217 outputs
Altmetric has tracked 25,388,229 research outputs across all sources so far. This one is in the 37th percentile – i.e., 37% of other outputs scored the same or lower than it.
So far Altmetric has tracked 11,236 research outputs from this source. They receive a mean Attention Score of 4.8. This one is in the 48th percentile – i.e., 48% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 332,741 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 47th percentile – i.e., 47% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 217 others from the same source and published within six weeks on either side of this one. This one is in the 42nd percentile – i.e., 42% of its contemporaries scored the same or lower than it.