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Comparative genomics of rice false smut fungi Ustilaginoidea virens Uv-Gvt strain from India reveals genetic diversity and phylogenetic divergence

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Abstract

False smut disease of rice caused by Ustilaginoidea virens, is an emerging threat to rice cultivation worldwide due to its detrimental effects on grain yield and quality. False smut disease severity was 4.44‒17.22% during a roving survey in Kharif 2016 in the four different rice ecosystems of Karnataka, India. Further, 15 pathogen isolates representing four different ecosystems were studied for their virulence and morphometric diversity. Among the 15 strains studied, most virulent strains Uv-Gvt was selected for whole genome sequencing in Illumina NextSeq 500 platform using 2 × 150 bp sequencing chemistry. The total assembled genome of Uv-Gvt was 26.96 Mb, which comprised of 9157 scaffolds with an N50 value of 15,934 bp and 6628 protein-coding genes. Next, the comparative genomic study revealed a similar gene inventory as UV-8b and MAFF 236576 strains reported from China and Japan, respectively. But, 1756 genes were unique to Uv-Gvt strain. The Uv-Gvt genome harbors 422 putative host–pathogen interacting genes compared to 359 and 520 genes in UV-8b and MAFF 236576 strains, respectively. The variant analysis revealed low genetic diversity (0.073‒0.088%) among U. virens strains. Further, phylogenetic analysis using 250 single copy orthologs genes of U. virens revealed a distinct phylogeny and an approximate divergence time. Our study, report the genomic resource of rice false smut pathogen from India, where the disease originated, and this information will have broader applicability in understanding the pathogen population diversity.

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Availability of data and materials

The Whole-Genome Shotgun project for U. virens strain Uv-Gvt was deposited in DDBJ/EMBL/GenBank under the accession number PGGP00000000 (Bio Project Id: PRJNA414696 and Bio-Sample ID: SAMN07807409). The version described in this paper is version PGGP00000000.2.

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Acknowledgements

This project was funded by the Early Career Research (ECR) Grant (Project Number: ECR/2017/000246) of Science and Engineering Research Board (SERB), Government of India to Pramesh D. We are thankful to Dr. Raju Soolanayakanahally, Saskatoon Research Center, Agriculture and Agri-food Canada, Canada and Dr. C. T. Manjunath Prasad, Wageningen Campus, Wageningen University and Research, The Netherlands for critically reviewing the manuscript.

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Authors and Affiliations

  1. Rice Pathology Laboratory, All India Co-ordinated Rice Improvement Program, Gangavathi, University of Agricultural Sciences, Raichur, 584 104, India

    Devanna Pramesh, Kondarajanahally M. Muniraju, Alase Saddamhusen, E. Chidanandappa, Masalavada K. Kumara & Huded Sharanabasav

  2. University of Agricultural Sciences, Bangalore, 560 065, India

    Muthukapalli K. Prasannakumar & H. B. Mahesh

  3. ICAR-Indian Institute of Oilseed Research, Hyderabad, 500 030, India

    H. D. Pushpa

  4. ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India

    Channappa Manjunatha

  5. ICAR- National Rice Research Institute, Cuttack, 753 006, India

    Manoj K. Yadav

  6. Molsys Pvt. Ltd., Bangalore, 560 064, India

    B. S. Rohith & Gaurab Banerjee

  7. School of Biotechnology, REVA University, Bangalore, 560 064, India

    Anupam J. Das

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  1. Devanna Pramesh
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Contributions

DP and MKP conceived the project, arranged the funds, designed the experiments and wrote the manuscript. KMM, AS, EC, MKK and HS conducted the survey, collected isolates, cultured and performed morphometric study. HBM, PHD, CM, MKY, BSR, GB and AJD submitted the raw data, carried out assembly, annotation, pathway analysis, phylogenetic study, SNP profiling, prepared tables and figures and wrote the manuscript. All authors read and approved the final manuscript for publication.

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Correspondence to Devanna Pramesh.

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Electronic supplementary material

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13205_2020_2336_MOESM1_ESM.jpg

Supplementary file1 Online Resource 1: Different stages of development of false smut disease of rice. a) development of pathogen mycelium inside the grain b) emergence of the mycelium with silvery membrane c) rupturing of silvery membrane d) development of pale yellow chlamydospores inside the membrane e) colour change from yellow to orange e) colour change from orange to olive green and finally to black (JPG 144 kb)

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Supplementary file5 Online Resource 5: List of predicted genes in Uv-Gvt genome (XLSX 16 kb)

Supplementary file6 (XLSX 514 kb)

Supplementary file7 (XLSX 148 kb)

Supplementary file8 (XLSX 11 kb)

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Supplementary file10 (DOCX 11 kb)

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Pramesh, D., Prasannakumar, M.K., Muniraju, K.M. et al. Comparative genomics of rice false smut fungi Ustilaginoidea virens Uv-Gvt strain from India reveals genetic diversity and phylogenetic divergence. 3 Biotech 10, 342 (2020). https://doi.org/10.1007/s13205-020-02336-9

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