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Tilletia indica  causes the disease Karnal bunt in wheat. The disease is under international quarantine regulations. Comparative mitochondrial (mt) genome analysis of  T .  indica  (KX394364 and DQ993184) and  T .  walkeri  (EF536375) has found 325 to 328 SNPs, 57 to 60 short InDels (from 1 to 13 nt), two InDels (30 and 61 nt) and five (>200 nt) presence/absence variations (PAVs) between the two species. The mt genomes of both species have identical gene order. The numbers of SNPs and InDels between the mt genomes of the two species are approximately nine times of the corresponding numbers between the two  T .  indica  isolates. There are eight SNPs between  T .  indica  and  T .  walkeri  that resulted in amino acid substitutions in the mt genes of  cob ,  nad2  and  nad5 . In contrast, there is no amino acid substitution in the mt genes of the  T .  indica  isolates from the SNPs found. The five PAVs present in  T .  indica  (DQ993184) are absent in  T .  walkeri . Four PAVs are more than 1 kb and are not present in every  T .  indica  isolate. Analysis of their presence and absence separates a collection of  T .  indica  isolates into 11 subgroups. Two PAVs have ORFs for the LAGLIDAG endonuclease and two have ORFs for the GIY-YIG endonuclease family, which are representatives of homing endonuclease genes (HEGs). These intron- encoded HEGs confer intron mobility and account for their fluid distribution in  T .  indica  isolates. The small PAV of 221 bp, present in every  T .  indica  isolate and unique to the species, was used as the genetic fingerprint for the successful development of a rapid, highly sensitive and specific loop mediated isothermal amplification (LAMP) assay. The simple procedure of the LAMP assay and the easy detection formats will enable the assay to be automated for high throughput diagnosis.

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Characterization of SNP and Structural Variations in the Mitochondrial Genomes of Tilletia indica and Its Closely Related Species Formed Basis for a Simple Diagnostic Assay