Tracking the evolution of holoparasitic plants: the smallest chloroplast genome ever sequenced in Cytinus hypocistis (Cytinaceae).

Plant plastid genomes are highly conserved. Parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, very few plastomes of parasites have been sequenced so far. Here we fill this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome. We sequenced the chloroplast genome of Cytinus hypocistis de novo using a shotgun approach on genomic DNA. Phylogenomic analyses based on coding regions were performed on Malvidae. Evolutionary codon models were fitted to estimate substitution rates and to infer selective pressures. Cytinus hypocistis has an extremely divergent genome that is the smallest sequenced to date (19Kb), with only twenty-three genes and no inverted repeat regions. Phylogenomic analysis confirms the position of Cytinus within Malvales.High substitution rates for all coding regions of Cytinus were detected. Some regions were inferred to be under relaxed negative selection, suggesting that plastome skiming is undergoing. Strong positive selection was detected for two regions (rpl22 and rps4) in the Cytinus lineage, suggesting a possible evolutionary role in the host-parasite arms race.