Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution

The present repository provides a FASTA resource with reference sequences of major repetitive DNA sequences from the genomes of Hydnora and Prosopanche species. This sequence list is complemented by a GFF file with detailed annotations for the included retrotransposons. 


The nuclear genomes of parasitic plants have undergone unique evolutionary trajectories to adapt to the heterotrophic lifestyle. These adaptations often involve large genomic alterations, potentially driven by repetitive elements. Despite the well-recognized role of repetitive DNAs as evolutionary forces in shaping plant genomes, their role in genome evolution of parasitic plants remains largely unexplored. To address this knowledge gap, we conducted the first analysis of repetitive DNAs in eleven genomes of Hydnoraceae, a family of mostly non-crop parasitizing holoparasites.

The observed repeat abundance profiles and presence-absence patterns align with the phylogenetic relationships, geographical distribution, and host shifts, suggesting a key role of repetitive DNAs in shaping Hydnoraceae genomes. The repetitive fraction of the two Hydnoraceae genera, Hydnora and Prosopanche, are fundamentally different: Whereas the eight analyzed Hydnora genomes are largely populated by long terminal repeat retrotransposons, particularly of the Tekay and Ogre type, the three Prosopanche repeatomes differ vastly in individual abundances, including P. bonacinae with massive amplifications of a single DNA transposon and P. panguanensis with over 15% 5S rDNA (as opposed to some Hydnoraceae with <0.1% 5S rDNA). Both extremely low and very high abundance of 5S rDNA challenges our current understanding for chromosome stabilization and rRNA transcription.

These genome dynamics suggest rapidly evolving repeat profiles, potentially being enhanced by the adaptation to the parasitic lifestyle. The heterogeneous abundance of rDNAs and DNA transposons in Hydnoraceae genomes needs further attention, with regard to repeat-driven evolution. This study lays the groundwork for future genomic explorations on Hydnoraceae, as well as heterotrophic plants and their nuclear genome composition in general.