Draft Genome Sequence of Two Monosporidial Lines of the Karnal Bunt Fungus
            <i>Tilletia indica</i>
            Mitra (PSWKBGH-1 and PSWKBGH-2)

Sharma, Pradeep; Tiwari, Ruchi; Saharan, M. S.; Sharma, Indu; Kumar, Jitender; Mishra, Sanjay; Muthusamy, Senthilkumar; Gupta, Raj Kumar; Jaiswal, Sarika; Iquebal, Mir Asif; Angadi, U. B.; Kumar, Neeraj; Fatma, Samar; Rai, Anil; Kumar, Dinesh

doi:10.1128/genomea.00928-16

Cited by 12 publications

(15 citation statements)

References 6 publications

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“…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 Two are unpublished and the other four were published too recently to be included in our analyses (Sharma et al 2016, Kumar et al 2017, Kumar et al 2018.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.…”

Section: Discussionmentioning

confidence: 99%

“…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.…”

Section: Candidate Markers For Detection Assaymentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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Tilletia species cause diseases on grass hosts with some causing bunt diseases on wheat (Triticum). Two of the four species infecting wheat have restricted distributions globally and are subject to quarantine regulations to prevent their spread to new areas. Tilletia indica causes Karnal bunt and is regulated by many countries while the nonregulated T. walkeri is morphologically similar and very closely related phylogenetically, but infects ryegrass (Lolium) and not wheat. Tilletia controversa causes dwarf bunt of wheat (DB) and is also regulated by some countries, while the closely related but non-regulated species, T. caries and T. laevis, both cause common bunt of wheat (CB). Historically, diagnostic methods have relied on cryptic morphology to differentiate these species in subsamples from grain shipments. Of the DNA-based methods published so far, most have focused on sequence variation among tested strains at a single gene locus. To facilitate the development of additional molecular assays for diagnostics, we generated whole genome data for multiple strains of the two regulated wheat pathogens and their closest relatives. Depending on the species, the genomes were assembled into 907 to 4633 scaffolds ranging from 24 Mb to 30 Mb with 7842 to 9952 gene models predicted. Phylogenomic analyses confirmed the placement of Tilletia in the Exobasidiomycetes and showed that T. indica and T. walkeri were in one clade whereas T. controversa, T. caries and T. laevis grouped in a separate clade. Single copy and species-specific genes were identified by orthologous group analysis. Unique species-specific genes were identified and evaluated as suitable markers to differentiate the quarantine and non-quarantine species. After further analyses and manual inspection, primers and probes for the optimum candidate genes were designed and tested in silico, for validation in future wet-lab studies.

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Section: Discussionmentioning

confidence: 99%

Section: Candidate Markers For Detection Assaymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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“…Although more SSRs need to be screened for the comprehensive study, the trend of amplification of SSR markers from two different genera indicated sufficient level of polymorphism. The draft genome sequence of Karnal bunt ( T. indica ) has been decoded (Sharma, Tiwari, Saharan, Sharma et al., ; Sharma, Tiwari, Saharan, Kumar et al., ), and will provide baseline data for mining perfect genome‐wide SSRs for genetic variability studies of Karnal bunt pathogen.…”

Section: Discussionmentioning

confidence: 99%

Development and validation of microsatellite markers for Karnal bunt (Tilletia indica) and loose smut (Ustilago segetum tritici) of wheat from related fungal species

Sharma

Shefali

Pandey

et al. 2018

Journal of Phytopathology

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Simple sequence repeats (SSRs) are preferred molecular markers because of their abundance, robustness, high reproducibility, high efficiency in detecting variation and suitability for high‐throughput analysis. In this study, an attempt was made to mine and analyse the SSRs from the genomes of two seed‐borne fungal pathogens, viz Ustilago maydis, which causes common smut of maize, and Tilletia horrida, the cause of rice kernel smut. After elimination of redundant sequences, 2,703 SSR loci of U. maydis were identified. Of the remaining SSRS, 44.5% accounted for di‐nucleotide repeats followed by 29.8% and 2.7% tri‐ and tetranucleotide repeats, respectively. Similarly, 2,638 SSR loci were identified in T. horrida, of which 20.2% were di‐nucleotide, 50.4% tri‐ and 20.5% tetra‐nucleotide repeats. A set of 65 SSRs designed from each fungus were validated, which yielded 23 polymorphic SSRs from Ustilago and 21 from Tilletia. These polymorphic SSR loci were also successfully cross‐amplified with the Ustilago segetum tritici and Tilletia indica. Principal coordinate analysis of SSR data clustered isolates according to their respective species. These newly developed and validated microsatellite markers may have immediate applications for detection of genetic variability and in population studies of bunt and smut of wheat and other related host plants. Moreover, this is first comprehensive report on molecular markers suitable for variability studies in wheat seed‐borne pathogens.

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“…The complete set of standard whole genome sequences for the Karnal bunt fungus T . indica with respect to intra-species monoteliosporic isolates, inter-stage monosporidial and dikaryon lines were obtained from the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov) to the local storage, having assembly accession numbers GCA_001645015.1, GCA_002220835.1, GCA_001689995.1, GCA_001689945.1 and GCA_001689965.1 for the isolates DAOM 236416 11 , RAKB_UP_1 12 , PSWKBGH_1, PSWKBGH_2 21 and PSWKBGD_1_3 respectively. A wide range of basic statistics was considered for each assembly and given below in Table 3.…”

Section: Methodsmentioning

confidence: 99%

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

Mishra

Maurya

Gupta

et al. 2019

Sci Rep

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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.

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Draft Genome Sequence of Two Monosporidial Lines of the Karnal Bunt Fungus Tilletia indica Mitra (PSWKBGH-1 and PSWKBGH-2)

Cited by 12 publications

References 6 publications

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

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

Development and validation of microsatellite markers for Karnal bunt (Tilletia indica) and loose smut (Ustilago segetum tritici) of wheat from related fungal species

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

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