Sugar Tech

, Volume 19, Issue 6, pp 604–615 | Cite as

Unraveling the Genetic Complexities in Gene Set of Sugarcane Red Rot Pathogen Colletotrichum falcatum Through Transcriptomic Approach

  • C. Naveen Prasanth
  • R. Viswanathan
  • Neethu Krishna
  • P. Malathi
  • A. Ramesh Sundar
  • Tanushree Tiwari
Research article


The transcriptome-based gene set expression of a unique sugarcane stalk infecting fungal pathogen reveals novels insights in deciphering the class of pathogenicity genes present in Colletotrichum falcatum. This study gains significance in understanding the genetic signature of this pathogen using RNA-Seq technology. A total of 53,410,513 reads (24,732 transcripts) specific to C. falcatum were generated, and 13,320 genes were predicted. Gene ontology distributions have been grouped into three domains as biological (3053), cellular (1601) and molecular functions (3444). KEGG annotations represented pathway biomolecules such as carbohydrates, lipids, nucleotides, amino acids, glycans, cofactors, vitamins, terpenoids and polyketides. The genes for virulence have been classified and grouped into candidate effectors, transition-specific and secondary metabolites, proteases, transporters and peptidases which revealed that C. falcatum transcripts encode a large number of secondary metabolites and membrane transporters. Gene enrichment analysis revealed that the number of transporters encoded by C. falcatum is significantly more as compared to that encoded by several other Colletotrichum spp. Phylogenomics analysis indicated that C. falcatum is closely related to C. graminicola and C. sublineola infecting related host plants, maize and sorghum, respectively. This study provides a comprehensive understanding of C. falcatum pathobiology and has identified many candidate genes/putative functions possibly required for its pathogenesis .


Colletotrichum falcatum Sugarcane RNA-Seq analysis 



The authors are grateful to the Director of ICAR-Sugarcane Breeding Institute, Coimbatore, for providing facilities and encouragement.


This study was partly funded by Outreach Project of ICAR, ALCOCERA.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical Standards

This article does not contain any studies with human participants or animals performed by any of the authors.

Data Access

All data contributing to this transcriptome initiative have been deposited at the NCBI under BioProject PRJNA272832. The accession number of Sequence Read Achieves (SRA) is SRR1765657.

Supplementary material

12355_2017_529_MOESM1_ESM.docx (82 kb)
Supplementary material 1 (DOCX 82 kb)


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Copyright information

© Society for Sugar Research & Promotion 2017

Authors and Affiliations

  • C. Naveen Prasanth
    • 1
  • R. Viswanathan
    • 1
  • Neethu Krishna
    • 2
  • P. Malathi
    • 1
  • A. Ramesh Sundar
    • 1
  • Tanushree Tiwari
    • 3
  1. 1.Division of Crop Protection, Sugarcane Breeding InstituteIndian Council of Agricultural ResearchCoimbatoreIndia
  2. 2.Indian Institute of Spices ResearchIndian Council of Agricultural ResearchCalicutIndia
  3. 3.Xcleris Genomics Pvt. Ltd.AhmadabadIndia

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