Abstract
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.
Highlights
T. indica causes the disease, Karnal bunt
This paper described the comparative analysis of the mt contig of a T. indica isolate obtained from generation sequencing with the reference mt genomes of T. indica (DQ993184) and T. walkeri (EF536375) which were obtained by conventional Sanger sequencing of libraries of DNA clones
The alignment of the mt genome contig of Ps2 with the reference mt genome of T. indica and T. walkeri showed that the mt genomes of the two species have identical gene order (Fig 1)
Summary
T. indica causes the disease, Karnal bunt. It replaces part of the seed with a black powdery mass containing millions of spores and produces a strong unpleasant odour like rotten fish. Risk analysis had indicated that the socio-economic impact of a Karnal bunt incursion from loss of export markets and costs of controlling the establishment and spread of the pathogen is huge in Australia and the EU countries [1, 2, 4, 5, 6]. History has shown that a Karnal bunt incursion in Arizona in 1996 had resulted in a ban of US wheat imports by 32 countries [7]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
