Diversity of repetitive elements in <i>Rutaceae</i> : implications for genome structure and potential phylogenetic signal

Plants of the genus Citrus in the family Rutaceae are widely cultivated across the globe. Classification within the Rutaceae family lacks a universally accepted framework. Repetitive DNA contains phylogenetic signals which can help trace back the evolution of species. We used low-coverage genome sequencing data from 60 Rutaceae species to analyze their repeatome and investigate phylogenetic relationships. We constructed a phylogenetic tree based on the replicability of repeat clusters and found that in Rutaceae species, the repeatomes constitutes, on average, 50% of the genome, with Athila (Gypsy) and SIRE (Copia) being the predominant LTR element families, present in low abundance in the repeatome of other flowering plants. Our findings showed that phylogenetic analyses relying on copy number clusters of repetitive elements exhibit significant limitations when applied to the Rutaceae family.