by Olga Kiryanova | Irek Gubaydullin | Alexey Chemeris | Ufa State Petroleum Technological University |
Institute of Petrochemistry and Catalysis, Ufa Federal Research Center | Institute of Biochemistry and
Genetics, Ufa Federal Research
Motivation and Aim: The classification and systematization of living organisms is currently
an actual task. The cytochrome oxidase gene was assumed as a reference region for the
living organisms. Here we propose a new method for DNA certification of living organisms
on the example of plants.
Methods and Algorithms: We have utilized in silico multiplex PCR analysis. Namely, we
have found the assumed primer annealing sites in a genome using the Knuth–Morris–Pratt
algorithm. The amplicons corresponding to the annealing sites were converted into a binary
format. The binary sequence is easy enough to translate into a barcode format.
Results: We have conducted a comparative analysis of the following plant genomes: wheat
(6 genomes), hevea (3 genomes), and arabidopsis (9 genomes). The proposed approach was
utilized to obtain barcodes for each group. Each set of barcodes indicated the differences
and similarities for certain plants. It should be pointed out, that different primers provide
different barcodes for the same genome. In this case, computer analysis makes it possible to
identify successful primers for the experimental PCR.
Conclusion: The presented DNA certification can reveal similarities and differences at the
level of large order taxa (species, family) however it more reliable for the certification of
cultivars. Hence, it allows to test several primers as well as to get an idea of the success
experiment. Thus, the proposed method provides a reliable and convenient way to store
genetic data in a digital format, and reduce the time consumption in PCR tests planning.
Acknowledgements: The study was funded by Russian Foundation for Basic Research
(17-44-020120).