STUDY OF NON-CODING AREAS OF THE DNA GENOME OF DIFFERENT ANIMAL SPECIES
Authors: Kopylov K. V. , Kopylova K. V. 
Published: July 2023

The introduction to the review article contains information that the genome is the totality of the DNA of a species, that is, the totality of all genes, non-coding regions of nuclear DNA and extrachromosomal genetic material, which includes mitochondrial, plastid DNA, plasmids, etc. An exon is a stretch of DNA within a gene that is translated into a mature matrix RNA (mRNA) molecule by transcription and splicing. They are separated by non-coding sequences (introns), that is, sections of DNA that are part of the gene, but, unlike exons, do not contain information about the amino acid sequence. In many organisms, only a small part of 2%–6% of the total genome sequence encodes proteins, and more than 90% of DNA consists of non-coding DNA sequences, satellite DNA, introns, tandem repeats, transposons, etc.). Non-coding sequences are sections of DNA whose sequence is not translated directly into the amino acid sequence of proteins.

As a research method, the authors declared a systematic approach to the study of factual materials, conducted a study of factual material and generalized their results.

The research results are as follows. The use of genotyping technologies and the use of molecular analysis methods made it possible to obtain an individual characteristic of an individual genotype – a DNA profile. Modern methods of DNA typing of genomes differ in complexity, reliability, and amount of information obtained. The most promising method is the analysis of polymorphism of hypervariable genome sequences, which makes it possible to obtain reproducible, informative profiles of genome fragments. DNA sequences are divided into multilocus (RAPD, AFLP, ISSR) and monolocus (STMS, SNP, SSCP) and others. The study of multilocus markers is based on the use of the polymerase chain reaction (PCR). The essence of the ISSR-PCR method (Inter-simple-sequence-repeats) is the use of microsatellite loci as primer firing sites that are complementary to microsatellite repeats (4–12 repeat units) and have 1–4 anchors at one 5' or 3' end. Such primers allow the amplification of DNA fragments located between microsatellite sequences. RAPD – markers (Random Amplified Polymophic DNA) – the essence of the method is to conduct a polymerase chain reaction using a primer with an arbitrary sequence of 10–12 nucleotides. For the synthesis of these primers, it is not necessary to know the specific nucleotide sequences of the genome, they must only meet the requirements for the ratio of GC pairs (about 60%) in length. AFLP (Amplified fragment length polymorphism) - amplified fragment length polymorphism (AFLP markers). The essence of the method is that DNA is treated with a combination of two restrictases. Specific adapters are ligated to sticky ends and the fragments are amplified using primers containing sequences in common with the adapters and 1–3 random bases. The set of resulting fragments depends on the restriction enzyme and primer extensions used. The primers have a fixed part with a complementary sequence of the adapter and the restriction site of the used endonuclease (~ 15 nucleotides), and a fragment at (at the 3'-end) with an arbitrary nucleotide sequence (2–4 nucleotides). The fixed part gives the primer stability, and the short part allows you to determine and control the proportion of ligated fragments. From each pair of primers, 75–100 fragments are amplified (AFLP - fingerprinting). AFLP markers are often inherited as tightly linked clusters in the centromere or telomere regions of chromosomes and have a dominant mode of inheritance. AFLP markers are used for genomic mapping in population and phylogenetic studies. Repeat sequences are divided into two classes: dispersed sequences and tandem repeats. Dispersed sequences, depending on their length, are classified into long interdispersion elements (LINEs) with a length of more than 1000 b. p. and short (SINEs) – less than 500 b. p. Depending on the length of the repeating fragments, they are divided into several classes: maxi (length over 5 x 105 b. p.), mini (length of the tandem repeating sequence 10–60 b. p.) and microsatellites with a motif length of 1–6 b. p. Minisatellites are used in "genomic fingerprinting" (DNA fingerprinting). The main mechanism for the emergence and existence of polymorphism in minisatellites is considered to be unequal crossing over and gene conversion, and high variability is associated with the mutation initiator flanking the repeat and activation of the mutagenic systems of the genome. The microsatellites are dispersed in tandem repeating mono-, di-, tri-, tetra-, and pentanucleotide sequences, which average less than 100 b. p. in size. They are a universal system of genetic markers for the analysis of configurations inherited at the level of nuclear DNA and used in animal husbandry.

The make the conclusion that molecular approaches make it possible to compare very distant organisms, and it is also important that the range of objects from which DNA suitable for analysis can be isolated continues to expand. The genome analysis technique, as well as the methods of phylogenetic data processing, are being developed and improved through the complex automation of the experimental part and the involvement of the mathematical apparatus of phylogenetic algorithms. Therefore, the planning of future research in the field of molecular phylogenetics is directly related to the accumulation of information about the nature of the evolution of genome regions studied in phylogenetics.