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Draft Genome Sequencing of Rhizoctonia solani Anastomosis Group 3 (AG3- PT) Causing Stem Canker and Black Scurf of Potato

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Abstract

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle being classified into fourteen reproductively incompatible anastomosis groups (AGs). AG3-PT (a potato subgroup) is associated with quantitative and qualitative yield losses through stem canker and black scurf in potato. Here we present the first draft sequence of the R. solani [AG3-PT] strain RS-20 with a G-C content of 48.3%. It consists of 11,431 total predicted protein coding regions including 181 tRNA and 31 rRNA coding genes. The initial pBLAST revealed more than 97% hits among AG groups where as only 1.7% of genes hit with other organisms. The R. solani genome is found to be dominated with tri mer repeats. The genome-wide evolutionary studies revealed the close association of AG3-PT with AG3. The draft sequence represents a helpful resource not only for understanding the core genes involved in pathogenecity but also evolution and adaptive behaviour within the R. solani species complex.

Resumen

Rhizoctonia solani es un hongo basidiomiceto del suelo con un estilo de vida necrotrófico que se clasifica dentro de los 14 grupos de anastomosis (AGs) de incompatibilidad reproductiva. AG3-PT (un subgrupo de papa) esta asociado con pérdidas de rendimiento cuantitativas y cualitativas por vía de cáncer de tallo y por costra negra en papa. Aquí presentamos la primera secuencia en borrador del R. solani [AG3-PT] variante RS-20 con un contenido de G-C de 48.3%. Consiste de 11,431 regiones totales de codificación predicha de proteínas incluyendo 181 tARN y 31 rARN genes de codificación. El pBLAST inicial reveló más del 97% de coincidencias entre los grupos AG, en donde tan solo el 1.7% de los genes coincidieron con otros organismos. El genomio de R. solani se encuentra dominado con repeticiones de trimeros. Los estudios de la evolución de la amplitud del genoma revelaron la asociación cercana de AG3-PT con AG3. La secuencia preliminar representa un recurso útil, no solo para entender los genes básicos involucrados en la patogenicidad, sino también la evolución y el comportamiento adaptativo dentro del complejo de la especie R. solani.

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Abbreviations

RS-20:

Rhizoctonia solani Strain 20

AG:

Anastomosis Groups

PT:

Potato type

NaOCl:

Sodium Hypochlorite

PDA:

Potato Dextrose Agar

CTAB:

Cetyi Trimethylammonium bromide

ITS:

Internal Transcribed Spacer

CDS:

Coding DNA Sequence

Mb:

Mega base (106 base)

Kb:

Kilo base (103 base)

MFS:

Major Facilitator Superfamily

MISA:

MIcroSAtellite

ANI:

Average Nucleotide Identity

PTP:

Peco Titre Plate

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Acknowledgements

This work was supported by Indian Council of Agriculture Research (ICAR), New Delhi, Government of India under the flagship programme “Structural and Functional Genomics of Potato and Its Pathogens”. Authors acknowledge the analysis input provided by ICAR-CPRI, CABin (Centre for Agriculture Bioinformatics).

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Authors and Affiliations

  1. Division of Crop Improvement, Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India

    Virupaksh U. Patil, Vanishree Girimalla, Vinay Bhardwaj & S. K. Chakrabarti

  2. Division of Plant Protection, Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India

    Vinay Sagar & S. K. Chakrabarti

Authors
  1. Virupaksh U. Patil
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  2. Vanishree Girimalla
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  3. Vinay Sagar
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  4. Vinay Bhardwaj
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  5. S. K. Chakrabarti
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Correspondence to Virupaksh U. Patil.

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The authors declare that they have no conflict of interest.

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Type culture is available with Dr. Vinay Sagar

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Patil, V.U., Girimalla, V., Sagar, V. et al. Draft Genome Sequencing of Rhizoctonia solani Anastomosis Group 3 (AG3- PT) Causing Stem Canker and Black Scurf of Potato. Am. J. Potato Res. 95, 87–91 (2018). https://doi.org/10.1007/s12230-017-9606-0

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  • DOI: https://doi.org/10.1007/s12230-017-9606-0

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