Potato super pangenome v1.0

Potato (Solanum sp., family Solanaceae) is the most important noncereal
food crop globally. It has over 100 wild relatives in the Solanum section
Petota, which features species with both sexual and asexual reproduction
and varying ploidy levels. A pangenome of Solanum section Petota composed
of 296 accessions was constructed including diploids and polyploids
compared via presence/absence variation (PAV). The Petota core (genes
shared by at least 97% of the accessions) and shell genomes (shared by 3
to 97%) are enriched in basic molecular and cellular functions, while the
cloud genome (genes present in less than 3% of the member accessions)
showed enrichment in transposable elements (TEs). Comparison of PAV in
domesticated vs. wild accessions was made, and a phylogenetic tree was
constructed based on PAVs, grouping accessions into different clades,
similar to previous phylogenies produced using DNA markers. A cladewise
pangenome approach identified abiotic stress response among the core genes
in clade 1+2 and clade 3, and flowering/tuberization among the core genes
in clade 4. The TE content differed between the clades, with clade 1+2,
which is composed of species from North and Central America with
reproductive isolation from species in other clades, having much lower TE
content compared to other clades. In contrast, accessions with in vitro
propagation history were identified and found to have high levels of TEs.
Results indicate a role for TEs in adaptation to new environments, both
natural and artificial, for Solanum section Petota.