Abstract

Repetitive sequences are major components of plant genomes and play key roles in genome size evolution and structural variation. Alstroemeria L. is a genus of monocotyledonous plants with giant genomes (1C ≈ 25 Gb), native to the Americas and distributed into two distinct lineages: the Brazilian/Argentinean clade and the Chilean grade. Despite their ancient separation and differences in heterochromatin distribution, all species share a highly conserved chromosome number (2n=16), with only minor variation in chromosome morphology. Here, we characterized the repetitive DNA fraction of six Chilean species, one Argentinean species, and two Brazilian species, and mapped the most abundant repeats on representative chromosomes from each lineage. LTR Ty3/gypsy Tekay retrotransposons were the predominant repetitive elements, accounting for 30.63–39.91% of the genome across all analyzed species and largely explaining genome size variation. Notably, despite their giant size, Alstroemeria genomes exhibited a relatively low overall proportion of repetitive DNA (up to ~68%), consistent with slow repeat removal and the accumulation of degraded sequences, as predicted for genomes of this size. Satellite DNA represented 0.23–3.42% of the genome, with most satellite families shared between the Brazilian and Chilean species. Nevertheless, despite the divergence of the Brazilian lineage approximately 9.2 million years ago, marked differences in satellite abundance and chromosomal distribution were observed. Our results indicate that giant genome evolution in Alstroemeria is characterized by long-term conservation of karyotype structure and transposable element composition, whereas satellite DNA constitutes a key dynamic component associated with heterochromatin diversification and longitudinal chromosomal differentiation between the Chilean and Brazilian lineages.