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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

Abstract

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.

Keywords

Rice sheath blight PHI-base Effectors Variants Necrotrophy Genome sequencing 

Notes

Acknowledgments

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

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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)

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High Resolution Image (TIF 260 kb)
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Online Resource 2

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

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High Resolution Image (TIF 4562 kb)
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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)

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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)
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Online Resource 5 Polymorphisms detected in BRS13 genome. (XLSX 1161 kb)
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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)
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Online Resource 9 List of pseudogenes containing premature stop codon under expanded category. (XLSX 10 kb)
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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)

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High Resolution Image (TIF 3297 kb)

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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

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