Comparative genomic analysis of monosporidial and monoteliosporic cultures for unraveling the complexity of molecular pathogenesis of Tilletia indica pathogen of wheat

Abstract

Tilletia indica (Ti) - a quarantined fungal pathogen of wheat and its pathogenesis is chiefly governed by pathogen effectors secreted inside the host plant. The de novo genome sequencing of several field isolates and stages available could be used for understanding the molecular pathogenesis. The presence of gaps and low coverage of assembled genomes poses a problem in accurate functional annotation of such functions. In the present study attempts were made to improve the Ti draft genome through reconciliation of globally available datasets of three highly virulent monoteliospore cultures of Ti field isolates. It has sequence depth of 107x and N50 scaffold size of 80,772 (more than 26 times as large as achieved in the draft assembly) with highest sequence contiguity, more accurate and nearly complete. Functional annotation revealed that Ti genome contains 9209 genes evolved with many expanded gene families and arranged mostly in a cluster. About 79% of Ti genes were orthologous to other basidiomycetes fungi, Around 7.93% proteins were having secretary signals and 6.66% were identified as highly virulent pathogenicity genes. Using improved Ti genome as a reference, the genomic variation was assessed with respect to repeats, SNPs/InDel, gene families and correct set of virulence associated genes during its life cycle. The comparative intra-species, inter-stage and inter-species genomic variation will have broader implications to understand the gene regulatory networks involved in growth, mating and virulence behaviour of Tilletia f. spp. and also for better appreciation of fungal biology and disease management.

Draft genome sequencing of Tilletia caries inciting common bunt of wheat provides pathogenicity-related genes

“…In earlier studies, Gypsys were the most common repeat element, which was reported in T. indica and T. horrida (Wang et al, 2018;Gurjar et al, 2019;Mishra et al, 2019). In fungi, the Gypsy group is the most common type of TE (Gorinsek et al, 2004).…”

Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis

“…The transposon types Gypsy followed by Copia , both belonging to the long terminal direct repeats (LTR) class of retrotransposons, were the most abundant in all three bunt species. Similarly, Gypsys were the most frequent TE reported in T. indica (Gurjar et al 2019 ; Mishra et al 2019 ) as well as in T. horrida (Wang et al 2018 ). Gypsy s are the most successful group of TEs in fungi (Gorinsek et al 2004 ) and plants (Sabot and Schulman 2006 ) and are capable to increase their number by autonomous transposition (Elliott and Gregory 2015 ).…”

Centenary of Soil and Air Borne Wheat Karnal Bunt Disease Research: A Review

“…Various candidate pathogenicity/virulence factors has been reported from the secretome of this TiK isolate such as mannitol dehydrogenase (TiMD), secretory lipase (TiL), transaldolase (TiTA), enolase (TiE), phosphoglucoseisomerase (TiPGI), thioredoxin (TiTR), peptidyl prolyl isomerase (TiPPI), and aspartate protease (TiAP) [ 64 ]. Consequently, Mishra et al [ 68 ] announced the first improved genome sequence of the monoteliosporic culture of Ti, consisting of the lowest number of 787 scaffolds with an estimated genome size of 31.83 Mbp, comprising of 9209 genes, of which 220 were virulence-associated genes (VAGs). Further, Gurjar et al [ 63 ], assembled a genome size of 33.7 Mb with a 10,113 predicted genes.…”