Exploring the repetitive DNA diversity in Solanum betaceum (Solanaceae)

Abstract The Solanaceae family, known for its diverse and economically important crops, includes the genus Solanum , which comprises 1245 species. Solanum betaceum (tree tomato), native to the Andes and cultivated worldwide, is a promising species due to its nutritional value and market potential. The Cyphomandra clade, which includes the tree tomato, is characterized by large genomes and chromosomes, where repetitive DNA elements (e.g., retrotransposons and satellite DNA) play crucial roles in genome organization and evolution. Despite its importance, genetic research on S. betaceum remains limited. This study addresses this knowledge gap by characterizing the repetitive DNA fraction to better understand intraspecific variation and development of chromosomal markers. Samples from five populations in northwestern Argentina were cultivated, and genome size was estimated via flow cytometry. Illumina HiSeq sequencing combined with RepeatExplorer2 analysis was applied to identify repetitive DNA elements. Cytogenetic techniques, including CMA/DAPI staining and fluorescence in situ hybridization (FISH), were employed to detect satellite DNA patterns. Genome size analysis revealed slight variation among populations (11.42 to 11.56 pg). Repetitive DNA accounted for 63.2% of the genome, with Ty3‐gypsy retrotransposons being the most abundant (51.5%). Satellite DNA and rDNA were less represented, comprising 1.0% and 0.3% of the genome, respectively. Population comparisons showed abundant proportions of repetitive DNA overall, with differences in Ty3‐gypsy‐Tekay and satellite DNA fractions. This study provides the first detailed characterization of the repetitive DNA landscape in S. betaceum , revealing intraspecific variation and delivering valuable genomic insights for future breeding and conservation efforts.