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