Functional & Integrative Genomics

, Volume 19, Issue 5, pp 799–810 | Cite as

Genome analysis provides insight about pathogenesis of Indian strains of Rhizoctonia solani in rice

  • Srayan Ghosh
  • Neelofar Mirza
  • Poonam Kanwar
  • Kriti Tyagi
  • Gopaljee JhaEmail author
Original Article


The Rhizoctonia solani species complex is comprised of strains belonging to different anastomosis groups and causes diseases in several economically important crops, including rice. However, individuals within same anastomosis group exhibit distinct morphological and pathological differences on the same host. In this study, we have sequenced the genome of two aggressive Indian strains (BRS11 and BRS13) belonging to AG1-IA anastomosis group and compared them with the available genome of R. solani AG1-IA. We identified several SNPs and Indels in both of these genomes, in comparison to the AG1-IA genome. Furthermore, we observed expansion and emergence of orthogroups in these Indian strains and identified those potentially associated with pathogenesis. Amongst them, transposable elements, cell wall degrading enzymes, transcription factors, and oxalate decarboxylase were noteworthy. The current study unravels genetic variations and identifies genes that might account for pathogenicity variations amongst R. solani strains.


Rice sheath blight PHI-base Effectors Variants Necrotrophy Genome sequencing 



SG acknowledges SPM fellowship from CSIR (Council of Scientific and Industrial Research, Govt. of India) while KT and PK acknowledge the SRF and Post-Doctoral Research fellowship from DBT (Department of Biotechnology, Govt of India) respectively. We are thankful to Dr. G.S. Laha, IIRR (Indian Institute of Rice Research, Hyderabad, India) and ITCC (Indian Type Culture Collection, New Delhi, India) for providing some of the R. solani strains used in this study. We also acknowledge Nucleome Informatics Pvt. Ltd. (Hyderabad) for assistance in genome sequencing. Further, the assistance of confocal microscopy, sequencing, plant growth and central instrumentation facilities at National Institute of Plant Genome Research (NIPGR) is acknowledged.

Author contributions

SG performed the isolation and characterization of Indian strains. NM and SG carried out genome analysis. SG and PK performed wet lab experiments and compiled the manuscript. SG, PK, NM, KT, and GJ drafted the manuscript. GJ planned and supervised the experiments.

Funding information

This work was supported by DBT, Government of India (BT/PR11532/AGIII/103/885/2014) as well as core research grant from NIPGR. The funders had no role in study design, data collection and analysis, decision to publish the manuscript.

Supplementary material

10142_2019_687_Fig6_ESM.png (136 kb)
Online Resource 1

Bioinformatics pipeline used in this study. The flowchart reflects strategies used for identification of i. SNPs and small Indels, ii. expansion and emergence of gene families and iii. Identification of potential pathogenicity determinants in BRS11 and BRS13. (PNG 135 kb)

10142_2019_687_MOESM1_ESM.tif (261 kb)
High Resolution Image (TIF 260 kb)
10142_2019_687_Fig7_ESM.png (1.8 mb)
Online Resource 2

Geographical distribution of different Indian R. solani strains used in the study. (PNG 1886 kb)

10142_2019_687_MOESM2_ESM.tif (4.5 mb)
High Resolution Image (TIF 4562 kb)
10142_2019_687_Fig8_ESM.png (23.7 mb)
Online Resource 3

The growth pattern of different Indian R. solani strains on PDA plates. The fungal sclerotia were grown on PDA plates and representative photographs of the plates during 6 and 10 days of incubation is provided. (PNG 24254 kb)

10142_2019_687_MOESM3_ESM.tif (32.9 mb)
High Resolution Image (TIF 33692 kb)
10142_2019_687_MOESM4_ESM.xlsx (1.1 mb)
Online Resource 4 Polymorphisms detected in BRS11 genome. (XLSX 1163 kb)
10142_2019_687_MOESM5_ESM.xlsx (1.1 mb)
Online Resource 5 Polymorphisms detected in BRS13 genome. (XLSX 1161 kb)
10142_2019_687_MOESM6_ESM.xlsx (11 kb)
Online Resource 6 Assembly statistics of unmapped reads. (XLSX 10 kb)
10142_2019_687_MOESM7_ESM.xlsx (19 kb)
Online Resource 7 Emerged orthogroups (gene families) in BRS11 and BRS13. (XLSX 18 kb)
10142_2019_687_MOESM8_ESM.xlsx (16 kb)
Online Resource 8 Expanded orthogroups (gene families) in BRS11 and BRS13. (XLSX 15 kb)
10142_2019_687_MOESM9_ESM.xlsx (11 kb)
Online Resource 9 List of pseudogenes containing premature stop codon under expanded category. (XLSX 10 kb)
10142_2019_687_Fig9_ESM.png (1.5 mb)
Online Resource 10

Prominent gene functions that have expanded/emerged in BRS11 and BRS13. The genes related to functions such as cell wall degradation, chromosomal rearrangement, multi-drug resistance, oxalate degradation, gene regulation, signaling, protein degradation and autophagy along with cellular detoxification were shown in different colored pies. Red arc depicts expanded and yellow arc represents emerged orthogroups. GCS: Gamma-glutamyl Cysteine Synthetase. (PNG 1563 kb)

10142_2019_687_MOESM10_ESM.tif (3.2 mb)
High Resolution Image (TIF 3297 kb)


  1. Ahvenniemi P, Wolf M, Lehtonen MJ, Wilson P, German-Kinnari M, Valkonen JPT (2009) Evolutionary diversification indicated by compensatory base changes in ITS2 secondary structures in a complex fungal species, Rhizoctonia solani. J Mol Evol 69:150–163CrossRefGoogle Scholar
  2. Ajayi-Oyetunde OO, Bradley CA (2018) Rhizoctonia solani: taxonomy, population biology and management of rhizoctonia seedling disease of soybean. Plant Pathol 67:3–17CrossRefGoogle Scholar
  3. Anderson JP, Sperschneider J, Win J, Kidd B, Yoshida K, Hane J, Saunders DGO, Singh KB (2017) Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors. Sci Rep 7:10410CrossRefPubMedPubMedCentralGoogle Scholar
  4. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477CrossRefPubMedPubMedCentralGoogle Scholar
  5. Banniza S, Rutherford MA (2001) Diversity of isolates of Rhizoctonia solani AG-1 1A and their relationship to other anastomosis groups based on pectic zymograms and molecular analysis. Mycol Res 105:33–40CrossRefGoogle Scholar
  6. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120CrossRefPubMedPubMedCentralGoogle Scholar
  7. Carling DE, Leine RH, Kebler KM (1987) Characterization of a new anastomosis group (AG-9) of Rhizoctonia solani. Phytopathology 77:1609–1612CrossRefGoogle Scholar
  8. Carling DE, Kuninaga S, Brainard KA (2002) Hyphal anastomosis reactions, rDNA-internal transcribed spacer sequences, and virulence levels among subsets of Rhizoctonia solani anastomosis group-2 (AG-2) and AG-BI. Phytopathology 92:43–50CrossRefPubMedGoogle Scholar
  9. Chibucos MC, Soliman S, Gebremariam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O’Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart SR, Skory CD, Ibrahim AS, Bruno VM (2016) An integrated genomic and transcriptomic survey of mucormycosis-causing fungi. Nat Commun 7:12218CrossRefPubMedPubMedCentralGoogle Scholar
  10. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6:80–92CrossRefGoogle Scholar
  11. Črešnar B, Petrič Š (2011) Cytochrome P450 enzymes in the fungal kingdom. Biochim Biophys Acta Proteins Proteomics 1814:29–35CrossRefGoogle Scholar
  12. Cubeta MA, Thomas E, Dean RA et al (2014) Draft genome sequence of the plant-pathogenic soil fungus Rhizoctonia solani anastomosis group 3 strain Rhs1AP. Genome Announc 2:e01072–e01014CrossRefPubMedPubMedCentralGoogle Scholar
  13. Doyle JJ, Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus (Madison) 12:13–15Google Scholar
  14. Emms DM, Kelly S (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16:157CrossRefPubMedPubMedCentralGoogle Scholar
  15. Ghosh S, Gupta SK, Jha G (2014) Identification and functional analysis of AG1-IA specific genes of Rhizoctonia solani. Curr Genet 60:327–341CrossRefGoogle Scholar
  16. Ghosh S, Kanwar P, Jha G (2018) Identification of candidate pathogenicity determinants of Rhizoctonia solani AG1-IA, which causes sheath blight disease in rice. Curr Genet 64:729–740CrossRefPubMedGoogle Scholar
  17. González García V, Portal Onco MA, Rubio Susan V (2006) Review. Biology and systematics of the form genus Rhizoctonia. Spanish J Agric Res 4:55–79CrossRefGoogle Scholar
  18. Guermache F, Rodier-Goud M, Caesar A, Héraud C, Bon MC (2012) Bi-fluorescence imaging for estimating accurately the nuclear condition of Rhizoctonia spp. Lett Appl Microbiol 54:568–571CrossRefPubMedGoogle Scholar
  19. Gupta A, Chattoo BB (2008) Functional analysis of a novel ABC transporter ABC4 from Magnaporthe grisea. FEMS Microbiol Lett 278:22–28CrossRefPubMedGoogle Scholar
  20. Hane JK, Anderson JP, Williams AH, Sperschneider J, Singh KB (2014) Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8. PLoS Genet 10(5):e1004281CrossRefPubMedPubMedCentralGoogle Scholar
  21. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kuninaga S, Yokosawa R (1985) DNA Base sequence homology in Rhizoctonia solani Kühn. Jpn J Phytopathol 51:127–132CrossRefGoogle Scholar
  23. Kuninaga S, Natsuaki T, Takeuchi T, Yokosawa R (1997) Sequence variation of the rDNA ITS regions within and between anastomosis groups in Rhizoctonia solani. Curr Genet 32:237–243CrossRefPubMedGoogle Scholar
  24. Kuninaga S, Carling DE, Takeuchi T, Yokosawa R (2006) Comparison of rDNA-ITS sequences between potato and tobacco strains in Rhizoctonia solani AG-3. J Gen Plant Pathol 66:2–11CrossRefGoogle Scholar
  25. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9:357–359CrossRefPubMedPubMedCentralGoogle Scholar
  26. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079CrossRefPubMedPubMedCentralGoogle Scholar
  27. Liang X, Moomaw EW, Rollins JA (2015) Fungal oxalate decarboxylase activity contributes to Sclerotinia sclerotiorum early infection by affecting both compound appressoria development and function. Mol Plant Pathol 16:825–836CrossRefPubMedGoogle Scholar
  28. Ma L, Chen Z, Huang DW, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA (2016) Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat Commun 7:10740CrossRefPubMedPubMedCentralGoogle Scholar
  29. MacPherson S, Larochelle M, Turcotte B (2006) A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev 70:583–604CrossRefPubMedPubMedCentralGoogle Scholar
  30. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536–540PubMedGoogle Scholar
  31. Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, Durbin R (2016) BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics 32:1749–1751CrossRefPubMedPubMedCentralGoogle Scholar
  32. Newman D (1939) The distribution of range in samples from a normal population, expressed in terms of an independent estimate of standard deviation. Biometrika 31:20–30CrossRefGoogle Scholar
  33. Ospina-Giraldo MD, Griffith JG, Laird EW, Mingora C (2010) The CAZyome of Phytophthora spp.: a comprehensive analysis of the gene complement coding for carbohydrate-active enzymes in species of the genus Phytophthora. BMC Genomics 11:525CrossRefPubMedPubMedCentralGoogle Scholar
  34. Pascual CB, Toda T, Raymondo AD, Hyakumachi M (2000) Characterization by conventional techniques and PCR of Rhizoctonia solani isolates causing banded leaf sheath blight in maize. Plant Pathol 49:108–118CrossRefGoogle Scholar
  35. Ponting CP, Schultz J, Milpetz F, Bork P (1999) SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res 27:229–232CrossRefPubMedPubMedCentralGoogle Scholar
  36. Raffaele S, Kamoun S (2012) Genome evolution in filamentous plant pathogens: why bigger can be better. Nat Rev Microbiol 10:417–430CrossRefPubMedGoogle Scholar
  37. Rose PW, Prlić A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK (2017) The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res 45:D271–D281CrossRefPubMedGoogle Scholar
  38. Sharon M, Kuninaga S, Hyakumachi M et al (2008) Classification of Rhizoctonia spp. using rDNA-ITS sequence analysis supports the genetic basis of the classical anastomosis grouping. Mycoscience 49:93–114CrossRefGoogle Scholar
  39. Sinclair JB (1970) Rhizoctonia solani: biology and pathology. In: Parmeter J. (ed) Rhizoctonia solani: biology and pathology. University of California Press, Berkeley, Los Angeles and London, pp 199–217Google Scholar
  40. Singh A, Rohila R, Savary S et al (2003) Short communications infection process in sheath blight of rice caused by Rhizoctonia solani. Indian Phytopathol 56:434–438Google Scholar
  41. Sperschneider J, Dodds PN, Gardiner DM, Singh KB, Taylor JM (2018) Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. Mol Plant Pathol 19:2094–2110CrossRefPubMedGoogle Scholar
  42. Stanke M, Waack S (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19:ii215–ii225CrossRefPubMedGoogle Scholar
  43. Stanke M, Schöffmann O, Morgenstern B, Waack S (2006) Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7:62CrossRefPubMedPubMedCentralGoogle Scholar
  44. Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637–644CrossRefPubMedGoogle Scholar
  45. States DJ, Gish W (1994) Combined use of sequence similarity and codon bias for coding region identification. J Comput Biol 1:39–50CrossRefPubMedGoogle Scholar
  46. Stodart BJ, Harvey PR, Neate SM, Melanson DL, Scott ES (2007) Genetic variation and pathogenicity of anastomosis group 2 isolates of Rhizoctonia solani in Australia. Mycol Res 111:891–900CrossRefPubMedGoogle Scholar
  47. Sumner DR (1996) Sclerotia formation by Rhizoctonia species and their survival. In: Rhizoctonia species: taxonomy, molecular biology, ecology, pathology and disease control, pp 207–215Google Scholar
  48. Taheri P, Gnanamanickam S, Höfte M (2007) Characterization, genetic structure, and pathogenicity of Rhizoctonia spp. associated with rice sheath diseases in India. Phytopathology 97:373–383CrossRefPubMedGoogle Scholar
  49. Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P (2015) Sambamba: fast processing of NGS alignment formats. Bioinformatics 31:2032–2034CrossRefPubMedPubMedCentralGoogle Scholar
  50. Thompson JD, Higgins DG, Gibson TJ (1994) Clustal-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680CrossRefPubMedPubMedCentralGoogle Scholar
  51. Thon MR, Pan H, Diener S, Papalas J, Taro A, Mitchell TK, Dean RA (2006) The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae. Genome Biol 7:R16CrossRefPubMedPubMedCentralGoogle Scholar
  52. Tiwari IM, Jesuraj A, Kamboj R, Devanna BN, Botella JR, Sharma TR (2017) Host delivered RNAi, an efficient approach to increase rice resistance to sheath blight pathogen (Rhizoctonia solani). Sci Rep 7:7521CrossRefPubMedPubMedCentralGoogle Scholar
  53. Urban M, Cuzick A, Rutherford K, Irvine A, Pedro H, Pant R, Sadanadan V, Khamari L, Billal S, Mohanty S, Hammond-Kosack KE (2017) PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database. Nucleic Acids Res 45:D604–D610CrossRefPubMedGoogle Scholar
  54. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide to methods and applications. Academic Press, Inc, pp 315–322Google Scholar
  55. Wibberg D, Jelonek L, Rupp O, Hennig M, Eikmeyer F, Goesmann A, Hartmann A, Borriss R, Grosch R, Pühler A, Schlüter A (2013) Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. J Biotechnol 167:142–155CrossRefGoogle Scholar
  56. Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Pühler A, Fogelqvist J, Varrelmann M, Schlüter A, Dixelius C (2016) Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes. BMC Genomics 17:245CrossRefPubMedPubMedCentralGoogle Scholar
  57. Xue M, Yang J, Li Z et al (2012) Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae. PLoS Genet 8:1002869CrossRefGoogle Scholar
  58. Yamauchi Y, Hasegawa A, Taninaka A, Mizutani M, Sugimoto Y (2011) NADPH-dependent reductases involved in the detoxification of reactive carbonyls in plants. J Biol Chem 286:6999–7009CrossRefPubMedGoogle Scholar
  59. Yang G, Li C (2012) General description of Rhizoctonia species complex. In: Cumagun CJ (ed) Plant pathology, pp 41–52Google Scholar
  60. Yoshida K, Saunders DGO, Mitsuoka C, Natsume S, Kosugi S, Saitoh H, Inoue Y, Chuma I, Tosa Y, Cano LM, Kamoun S, Terauchi R (2016) Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements. BMC Genomics 17:370CrossRefPubMedPubMedCentralGoogle Scholar
  61. Zhao Z, Liu H, Wang C, Xu JR (2013) Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics 14:274CrossRefPubMedPubMedCentralGoogle Scholar
  62. Zheng A, Lin R, Zhang D, Qin P, Xu L, Ai P, Ding L, Wang Y, Chen Y, Liu Y, Sun Z, Feng H, Liang X, Fu R, Tang C, Li Q, Zhang J, Xie Z, Deng Q, Li S, Wang S, Zhu J, Wang L, Liu H, Li P (2013) The evolution and pathogenic mechanisms of the rice sheath blight pathogen. Nat Commun 4:1424CrossRefPubMedPubMedCentralGoogle Scholar
  63. Zhou B, Bailey A, Niblett CL, Qu R (2016) Control of brown patch (Rhizoctonia solani) in tall fescue (Festuca arundinacea Schreb.) by host induced gene silencing. Plant Cell Rep 35:791–802CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchNew DelhiIndia

Personalised recommendations