3 Biotech

, 9:219 | Cite as

De novo genome sequencing and secretome analysis of Tilletia indica inciting Karnal bunt of wheat provides pathogenesis-related genes

  • Malkhan Singh Gurjar
  • Rashmi AggarwalEmail author
  • Abhimanyu Jogawat
  • Deepika Kulshreshtha
  • Sapna Sharma
  • Amolkumar U. Solanke
  • Himanshu Dubey
  • Rakesh Kumar Jain
Original Article


Tilletia indica is an internationally quarantined fungal pathogen causing Karnal bunt of wheat. The present study carried out that the whole genome of T. indica was sequenced and identified transposable elements, pathogenicity-related genes using a comparative genomics approach. The T. indica genome assembly size of 33.7 MB was generated using Illumina and Pac Bio platforms with GC content of 55.0%. A total of 1737 scaffolds were obtained with N50 of 58,667 bp. The ab initio gene prediction was performed using Ustilago maydis as the reference species. A total number of 10,113 genes were predicted with an average gene size of 1945 bp out of which functionally annotated genes were 7262. A total number of 3216 protein-coding genes were assigned in different categories. Out of a total number of 1877 transposable elements, gypsy had the highest count (573). Total 5772 simple sequence repeats were identified in the genome assembly, and the most abundant simple sequence repeat type was trinucleotide having 42% of total SSRs. The comparative genome analysis suggested 3751 proteins of T. indica had orthologs in five fungi, whereas 126 proteins were unique to T. indica. Secretome analysis revealed the presence of 1014 secretory proteins and few carbohydrate-active enzymes in the genome. Some putative candidate pathogenicity-related genes were identified in the genome. The whole genome of T. indica will provide a window to understand the pathogenesis mechanism, fungal life cycle, survival of teliospores, and novel strategies for management of Karnal bunt disease of wheat.


Karnal bunt Wheat Tilletia indica Whole genome sequencing Secretome Pathogenesis-related genes 



The authors are highly thankful to ICAR-Consortium Research Platform (CRP) on Genomics (ICAR-G/CRP-Genomics/2015-2720/IARI-12-151) for funding this work. We are also highly thankful to Director, Joint Director (Research), ICAR-Indian Agricultural Research Institute, New Delhi for providing guidance and facilities for carry out this study. Authors are also thankful to Eurofins Genomics India Pvt. Ltd., Bangalore, India for whole genome sequencing.

Author contributions

MSG and RA were involved in conceptualization of project, whole genome sequencing, and data compilation. AJ, DK, SS, and HD performed DNA extraction, assembly, gene prediction, annotation, phylogenetic analysis, and bioinformatics analysis. RA and MSG supervised the genome sequencing data and drafted the manuscript. AKS and RKJ were involved in critical inputs and finalization of manuscript. All authors have read and contributed for final manuscript.

Compliance with ethical standards

Conflict of interest statement

The authors declare that they have no conflict of interest in the publication.

Availability of data and materials

The whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers MBSW00000000. The version described in this paper is version MBSW01000000.

Supplementary material

13205_2019_1743_MOESM1_ESM.xls (352 kb)
Online Resource 1 Gene ontology in the genome of T. indica (XLS 351 kb)
13205_2019_1743_MOESM2_ESM.xlsx (128 kb)
Online Resource 2 Identified Pathways in the genome of T. indica (XLSX 124 kb)
13205_2019_1743_MOESM3_ESM.xls (216 kb)
Online Resource 3 Identified transposable elements in the genome (XLS 216 kb)
13205_2019_1743_MOESM4_ESM.pdf (733 kb)
Online Resource 4 Predicted of secretory effectors proteins (PDF 732 kb)
13205_2019_1743_MOESM5_ESM.xls (741 kb)
Online Resource 5 Identified small-secreted proteins in the genome (XLS 741 kb)
13205_2019_1743_MOESM6_ESM.xls (404 kb)
Online Resource 6 Carbohydrate-active enzymes (XLS 404 kb)
13205_2019_1743_MOESM7_ESM.xlsx (54 kb)
Online Resource 7 Functional annotation of genes through PHI data base (XLSX 54 kb)


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Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  • Malkhan Singh Gurjar
    • 1
  • Rashmi Aggarwal
    • 1
    Email author
  • Abhimanyu Jogawat
    • 1
  • Deepika Kulshreshtha
    • 1
  • Sapna Sharma
    • 1
  • Amolkumar U. Solanke
    • 1
    • 2
  • Himanshu Dubey
    • 1
    • 2
  • Rakesh Kumar Jain
    • 1
  1. 1.Fungal Molecular Biology Laboratory, Division of Plant PathologyICAR-Indian Agricultural Research InstituteNew DelhiIndia
  2. 2.ICAR-National Research Centre on Plant BiotechnologyNew DelhiIndia

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