PANGENOMICS OF PLANTS

The concept of plant pangenomes appeared in 2007, but the preliminary pangenomes of corn and soybeans were created in 2010. First pangenomes of three plant species (Brassica rapa, Glycine soja, and Oryza sativa) were constructed only in 2014. In 2016, several species from Populus and Oryza were used to construct pangenomes for these genera, which formally made those pangenomes super-pangenomes long before the concept of super-pangenomes was described in 2020, already dealing with a taxon having the rank of genus. In the same year (2020), the first Malus pangenome was constructed based on sequenced genomes with phased assembly of haplotypes, and because two more wild apple tree species were involved, that phased pangenome also became a Malus super-pangenome. In 2022, hyper-pangenomes were generated for representatives of genera Musa and Ensete of the Musaceae as well as a Citrus hyper-pangenome using data on genomes of several genera from the Rutaceae. To date, more than 150 pangenomes of all these types have been constructed, and there is a clear growth trend in the number of pangenomes being built. At the same time, it can be predicted that the number of conventional pangenomes will grow at a slower rate than that of phased super-pangenomes because the latter are of the greatest interest for breeding to create varieties of agricultural plants that are high-yielding and resistant to adverse environmental factors. The reason for this interest in plant pangenomes is that reference genomes of individual species, owing to mosaic assembly of determined nucleotide sequences, no longer satisfy the needs of breeders because these data are essentially incomplete information about genomic diversity characteristic of a species/genus or a group of closely related genera of the same family in the form of a gene repertoire consisting of different categories of genes: core, softcore, disposable, and private genes. Although the first two categories mostly ensure the main metabolism, the other two are responsible for secondary metabolism and largely determine the diversity of forms, e.g., by allowing a plant to adapt to its changing environmental conditions. It can be said that agricultural science has already entered the pangenomic era. The most correct selection of different cultivars for breeding should now be based on pangenomic data (including super- and hyper-pangenomes) constructed on the basis of a chromosomal assembly of diploid genomes with phased haplotypes. In fact, genomics, even if it retains its former name, should ideologically turn into pangenomics.