Nuclear genome profiling of two species of <i>Epidendrum</i> (Orchidaceae): genome size, repeatome, and ploidy

Characterizing genomic properties such as genome size, ploidy level, heterozygosity, and repetitive DNA proportion and composition without relying on genome assembly is crucial for profiling the genomes of non-model species. This study compares genome profiles of <i>Epidendrum anisatum</i> and <i>Epidendrum marmoratum</i>, using flow cytometry and <i>k</i>-mer analysis approaches, as well as bioinformatic ploidy-level estimation and repeatome characterization. Multiple depths of coverage, <i>k</i> values, and software tools for genome size estimation were explored and contrasted with cytometry genome size estimations. Cytometry and <i>k</i>-mer analyses yielded a consistently higher genome size for <i>E. anisatum</i> (2.59 Gb) than <i>E. marmoratum</i> (1.13 Gb), a 2.3-fold genome size difference. Both species were identified as diploid with no evidence of partial endoreplication. The genomes of both species were found to be highly repetitive (63%-73%) and heavily dominated by Ogre Ty3-gypsy retrotransposons. Additionally, the genome of <i>E. anisatum</i> was characterized by the presence of a 172 bp satellite (<i>AniS1</i>), which represented 11% of the genome size. Together, both Ty3-gypsy transposons and <i>AniS1</i> shape the genome size difference between the two genomes. This study highlights the importance of using flow cytometry, cytogenetic approaches, and bioinformatics techniques in conjunction for genome profiling.