The repeatome landscape in the "Saccharum complex"

The "Saccharum complex" comprises several closely related genera (Tripidium/Erianthus, Miscanthus and Narenga) which may hybridize with Saccharum, contributing to the origin of modern sugarcane. Sugarcane (Saccharum spp.) has one of the most complex crop genomes, shaped by interspecific hybridization, extreme polyploidy, and extensive chromosomal rearrangements. Research has found that repetitive DNA constitutes a large fraction of its genome. However, the dynamics, distribution, and evolutionary significance of these elements across the "Saccharum complex" are yet to be resolved.

Here, we analyzed data from 30 genotypes, representing nine Saccharum species, several modern sugarcane cultivars and individuals from Erianthus, Miscanthus and Narenga. Repetitive sequences were identified using RepeatExplorer2. Repeat lineage evolution was assessed through comparative clustering, correlation analyses, and repeat-based phylogenetic reconstruction. LTR retrotransposons (LTR-RTs) were further examined in fully assembled genomes of S. officinarum, S. spontaneum, and the cultivar R570 using DANTE.

Repetitive DNA content ranged from 42.5% to 59.7%, with LTR-RTs the dominant fraction. Ty3 LTR-RTs, particularly Tekay, and Ty1 LTR-RTs, mainly SIRE, exhibited most interspecific variation. A homogeneous repeatome was found in S. officinarum, while S. spontaneum exhibited divergence among cytotypes. Satellite DNAs were abundant and largely taxon-specific, yet all species shared a highly conserved 137-bp centromeric repeat. Repeat abundance was strongly correlated with genome size, underscoring the central role of transposable element proliferation in genome expansion. Repeat-based phylogenies are (mainly) in line with published Saccharum phylogenies. Structural analyses of LTR-RTs revealed lineage-specific signatures of recent amplification, especially within SIRE and Tekay.

Together, these results show that the Saccharum repeatome reflects both shared ancestry and extensive lineage-specific diversification. Repetitive DNA has played a major role in genome expansion and retains signatures associated with species differentiation and hybridization. The repeat families identified here provide valuable cytogenetic and genomic resources and offer an evolutionary framework which is key to understanding polyploid genome dynamics in sugarcane.