Multiplex in silico RAPD-Analysis for Genome Barcoding

Abstract

In this work, we propose a new method for identifying organisms of multiplex polymerase chain reaction (PCR) with arbitrary primers in silico (multiplex in silico RAPD-analysis) for the unique identification of living organisms. The results of computer modeling search of possible primer annealing sites in genomic DNA, and their convertation into the genomic barcode format, are proposed. These data with information about used primers that can be unique for genomes. A comparative analysis of genomic barcodes of species of related plant species was carried out in order to classify them on the level of species and lines in the future. A pairwise analysis of the location of the same or similar amplicons within different subgenomes and genomes is presented. The genomes of wheat and Aegilops in FASTA files format are presented as the research samples. The proposed method makes possible to predict the success of the multiplex polymerase chain reaction using special primers in the laboratory. This technology allows the analysis of the entire genomic DNA, rather than fragments of the genome.