Comparative analysis of repetitive sequences among species from the potato and the tomato clades

The genus Solanum includes important vegetable crops and their wild relatives. Introgression of their useful traits into elite cultivars requires effective recombination between hom(e)ologues, which is partially determined by genome sequence differentiation. In this study Gaiero et al. compared the repetitive genome fractions of wild and cultivated species of the potato and tomato clades in a phylogenetic context.

All-to-all similarity comparison of sequence reads from Solanum species based on cluster composition across all 13 species included in this study.
All-to-all similarity comparison of sequence reads from Solanum species based on cluster composition across all 13 species included in this study. The bar plots show the size of the repetitive fraction of the genome, represented as a percentage of each genome. Different colours represent different repeat families. (A) Relative abundance of interspersed repeats. (B) Relative abundance of tandem repeats. See Gaiero et al. 2018 for species codes.

Repeat abundance and genome size were correlated, and the larger genomes of species in the tomato clade were found to contain a higher proportion of unclassified elements. Families and lineages of repetitive elements were largely conserved between the clades, but their relative proportions differed. The most abundant repeats were Ty3/Gypsy elements.

The repeat profiles in Solanum seem to be very similar despite genome differentiation at the level of collinearity. Removal of transposable elements by unequal recombination may have been responsible for structural rearrangements across the tomato clade. Sequence variability in the tomato clade is congruent with clade-specific amplification of repeats after its divergence from S. etuberosum and potatoes. The low differentiation among potato and its wild relatives at the level of interspersed repeats may explain the difficulty in discriminating their genomes by genomic in situ hybridisation techniques.

Reference List

Gaiero, P., Vaio, M., Peters, S. A., Schranz, M. E., de Jong, H., & Speranza, P. R. (2018). Comparative analysis of repetitive sequences among species from the potato and the tomato clades. Annals of Botany. https://doi.org/10.1093/aob/mcy186