The study of pangenomes and super-pangenomes is a necessary requirement for the creation of promising intragenic and cisgenic plants, as well as the disclosure of the nature of heterosis
Authors: Chemeris D.A. , Kuluev B.R. , Garafutdinov R.R. , Gerashchenkov G.A. , Baymiev An.Kh. , Baymiev Al.Kh. , Chemeris A.V. 
Published: December 2023

Appearance in the middle of 1990s the phrase "post-genomic era" was premature, since sequenced at that time (and for the most part now) the so-called complete genomes of higher organisms are, according to the current definition of the term "genome", DNA sequences of a half set of chromosomes, moreover, assembled from fragments of paired chromosomes, joined in a chaotic manner, which allows them to be considered "quasi-haploid" genomes or "quasigenomes", giving only half genetic information about a particular organism, whereas its the phenotype determines only the complete set of chromosomes, and thus for the whole set of DNA in all chromosome it is proposed to use the new term "dinome". In biological science (physico-chemical biology), it is possible to distinguish the "pre-nucleic" and "nucleic" eras, the boundary between which is the epoch-making article by F.Miescher far ahead of its time. Mischer discovered in 1869 an unknown substance rich in phosphorus, which he called "nuclein", and which became known much later as DNA. The "nucleic era", in turn, can be divided into a number of periods: "tetrad", "pre-spiral", "pre-genomic", "quasigenomic", "pangenomic", "genomic" or more precisely "dinomic", which is just beginning. Despite the reduction in the cost of whole genome sequencing and the acceleration of this process over the past couple of decades by approximately millions of times, as well as despite a noticeable increase in its accuracy, a radical change in the worldview of scientists due to the urgent need to sequence diploid genomes and assemble their nucleotide sequences in a phased/haplotyped format has not yet occurred, and number of similar dinomes including such for plants have been sequenced extremely little yet. And this requires an ideologically new approach to sequencing nuclear DNA from the entire set of chromosomes. It should be recognized that dinomes are the future due to the fact that with quasi-haploid sequencing it is often impossible to determine the cis- and transpositions of individual nucleotide substitutions and, accordingly, to establish the true protein sequences encoded by them, which can lead to a misconception about their catalytic or other features. There is also an understanding that the so-called reference or reference genomes of higher organisms do not provide complete information about the variations of nucleotide sequences inherent in different representatives of a particular species/varieties /lines in this connection, a new trend is gaining strength in the form of sequencing of pangenomes of the species (biological) or super-pangenomes of the genus (biological), which allow identifying characteristic core genes for all, as well as some additional genes inherent in some, the ratio of which in the dinome for individual samples may be almost equal. Moreover, the sequencing of pangenomes is extremely important since the information obtained can be used to improve crops to increase their yield, including for the purpose of creating cisgenic plants based on such data, under certain conditions (in the absence of foreign DNA in the form of marker and selective genes, as well as other auxiliary sequences) aren’t GMO. Knowledge of pangenomes of various lines can contribute to the production of highly heterotic hybrids of agronomically important plants, the hybrid power in which (so far theoretically) can be fixed with the help of artificial apomixis using CRISPR/Cas genomic editing technology. At the same time, the sequencing of pangenomes sheds light on the emergence of the hybrid force effect, which gives reason to put forward the "pangenomic theory of heterosis", since in this case, due to crossing over, according to unknown laws, a certain (successful) consolidation of heterogeneous genomes occurs.