In the reference genomes of different species, the frequency of microsatellite (GAG) 6C is the highest among the studied sequences; the frequency of homology sites to long terminal repeats of two retroviruses, SIRE 1 and Sabrina, is the lowest, but it is not associated with the results of experimental studies of polymorphism spectra of their flanking genomic fragments (Tables 1, 2). Thus, there is no direct relationship between co-localization of homology sites to them in reference genomes and mobile genetic elements as well as their polymorphism in experimental studies (Tables 1, 2). At the same time, a certain negative association between the frequency of co-localization of G4 quadruplexes in the regions of reference genomes flanked by sequences used as primers in the experiment and the polymorphism of their spectra in polymerase chain reaction was found in both species (Tables 1, 2). The marked differences between the frequency of G4 quadruplexes in the considered regions of domestic dog and jumping lizard reference genomes are consistent with the data on the species specificity of their representation (Marsico et al., (2019)).
It is known that the source of microRNAs is mobile genetic elements and this is the essential pathway of their influence on the formation of regulatory networks that determine gene expression profiles and their dynamics in multicellular organisms (Ali et al., (2021)).
Interestingly, our studies revealed a certain negative association between the frequency of homology sites to microRNA and the density of G4 quadruplexes in the considered fragments of the reference genomes of domestic dog and jumping lizard (Tables 1, 2). Only the sites flanked by the inverted repeat of the microsatellite (GAG) 6C, the frequency of which is significantly higher than the other considered microsatellites in the reference genomes of both species, fall out of this association (Tables 1, 2). The observed interspecific differences in the frequency of homology sites to microRNAs and G4 quadruplexes in the studied regions of the reference genomes of domestic dog and jumping lizard are not consistent with the notion that these two genomic characteristics are generally closely related to each other (Chan et al., 2018).
The nucleotide sequence of microsatellite (GAG)n refers to DNA regions potentially predisposed to the formation of triplexes (purine-pyrimidine tracks) that play an essential role in the formation of secondary DNA structures, DNA:RNA binding, chromatin organization, and gene expression regulation (Postepska-Igielska et al., 2020). The diversity of functional involvement of such sequences in the structural and functional organization of the genome can apparently explain the differences in their distribution in the reference genomes of both species from other microsatellite sequences.
In general, comparative analysis of polymorphism of genomic DNA fragments of two species in experimental studies of population-genetic structures using ISSR-PCR and IRAP-PCR markers and distribution of homology sites to nucleotide sequences used as primers in PCR in reference genomes of domestic dog and jumping lizard suggests a certain association between G4 quadruplex densities and polymorphism of such markers.
G-quadruplexes are known to be an integral part of complex regulatory systems, closely related to the movement of retrotransposons in mammals (Sahakyan et al., (2017)). Evidence is accumulating that there is a delicate balance between genome instability caused by G4 quadruplexes and its repair processes stimulated by the same G4 quadruplexes. It is suggested that this is what ensures the stability of G4 structures in vitro and in vivo (Pavlova et al., (2021)), their certain conservatism (Capra et al., (2010); Zybaĭlov et al., (2013)). High density of G4 quadruplexes in the "hot spots" of mononucleotide substitutions, which does not always coincide with the increased recombination frequency, indicates the possible influence of nucleotide context and various features of DNA secondary structure formation (Glazko et al., (2021)).
Our studies suggest that despite the polyfunctionality and complexity of the distribution of the considered nucleotide motifs, the preliminary analysis of reference genomes on the distribution of homology sites to potential primers and their associations with the frequency of G4 quadruplexes can improve the efficiency of ISSR-PCR and IRAP-PCR markers in population genetic studies.