Nuclear genome profiling of two Mexican orchids of the genus Epidendrum

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. Little is known about the nuclear genome of the large neotropical orchid genus Epidendrum . This study compares genome profiles of Epidendrum anisatum and E. marmoratum, using flow cytometry and k-mer analysis approaches, as well as bioinformatics ploidy level estimation and repeatome characterization. Multiple depths of coverage, k values, and k-mer-based tools for genome size estimation were explored. A 2.3-fold genome size difference was found between the two species, ranging from 2.35 to 2.80 Gb (x̂ = 2.58 Gb) for E. anisatum and from 0.99 to 1.24 Gb (x̂ = 1.11 Gb) for E. marmoratum . Both species were identified as diploid with no evidence of strict partial endoreplication. The most important aspects to be taken into account to improve genome size estimation were heterozygosity, depth of coverage, and the maximum k-mer coverage. The genomes of both species were found to be highly repetitive (63–73%) and heavily dominated by Ty3-gypsy retrotransposons, particularly those of the Ogre family. Additionally, the genome of E. anisatum was characterized by the presence of a 172 bp satellite ( AniS1 ), which represented 11% of the genome size. Together, both Ty3-gypsy transposons and AniS1 shape the genome size difference between the two Epidendrum genomes. This study provides the first genome profiling for species in the genus Epidendrum , but also highlights the importance of using flow cytometry, cytogenetic approaches and bioinformatics techniques in combination for genome profiling.