Draft genome sequence of Karnal bunt pathogen (Tilletia indica) of wheat provides insights into the pathogenic mechanisms of quarantined fungus

Abstract

Karnal bunt disease in wheat is caused by hemibiotrophic fungus, Tilletia indica that has been placed as quarantine pest in more than 70 countries. Despite its economic importance, little knowledge about the molecular components of fungal pathogenesis is known. In this study, first time the genome sequence of T. indica has been deciphered for unraveling the effectors’ functions of molecular pathogenesis of Karnal bunt disease. The T. indica genome was sequenced employing hybrid approach of PacBio Single Molecule Real Time (SMRT) and Illumina HiSEQ 2000 sequencing platforms. The genome was assembled into 10,957 contigs (N50 contig length 3 kb) with total size of 26.7 Mb and GC content of 53.99%. The number of predicted putative genes were 11,535, which were annotated with Gene Ontology databases. Functional annotation of Karnal bunt pathogen genome and classification of identified effectors into protein families revealed interesting functions related to pathogenesis. Search for effectors’ genes using pathogen host interaction database identified 135 genes. The T. indica genome sequence and putative genes involved in molecular pathogenesis would further help in devising novel and effective disease management strategies including development of resistant wheat genotypes, novel biomarkers for pathogen detection and new targets for fungicide development.

Genome sequencing and comparison of five Tilletia species to identify candidate genes for the detection of regulated species infecting wheat

“…Currently there are six other genomes listed on GenBank for T. indica strains, all originating from India, none with annotations. Two are unpublished and the other four were published too recently to be included in our analyses (Sharma et al 2016, Kumar et al 2017, Kumar et al 2018. There is also a genome for one T. horrida strain originating from China.…”

“…After manual inspection and verification, only a few candidates with appropriate primer/probe sites were identified and suggested for further wet lab validation in a future study: one for T. controversa, two for T. laevis, one for T. indica, three for T. walkeri and seventeen for T. caries (Table 4). The designed primers and probes were mapped back to all genome assemblies, including those of T. indica (Sharma et al 2016;Kumar et al 2017;Kumar et al 2018) and T. horrida (Wang et al 2015) available on NCBI, and were found to be indeed unique for detecting the intended species for which they were designed (data not shown). To assign putative function to these candidate genes, we analyzed the protein sequence with InterProScan.…”

“…Although no genome assemblies were publicly available for the genus Tilletia when this study was initiated, there are now genomes for T. indica or T. walkeri (Tan et al 2016;Sharma et al 2016;Kumar et al 2017;Kumar et al 2018) and T. horrida (Wang et al 2015), but no other species. We have sequenced, annotated and compared the whole genomes of three strains of T. indica, two strains of T. walkeri, two strains of T. controversa, one strain of T. caries and two strains of T. laevis.…”

Secretome Analysis Identifies Potential Pathogenicity/Virulence Factors of Tilletia indica, a Quarantined Fungal Pathogen Inciting Karnal Bunt Disease in Wheat

“…Sequenced genome TiK isolate of T. indica was used for identification of candidate pathogenicity/virulence factors homologs using BLASTP search. Identified putative pathogenicity/virulence factors from T. indica genome were subjected to further sequence‐and structure‐based functional annotation.…”

“…With this view, the present study was carried out with the aim of comparing the secretomes of T. indica isolates showing differential virulence behavior. Results obtained by comprehensive secretome analysis have been further complemented with the de novo genome sequence generated through the hybrid approach of Illumina HiSeq 2000 and PacBio single molecule real time (SMRT) sequencing . Identified homologs of candidate pathogenicity/virulence factors from T. indica genome were further subjected to sequence‐ and structure‐based functional annotation.…”