Diverse trajectories of plastome degradation in holoparasitic Cistanche and the whereabouts of the lost plastid genes

The plastid genomes (plastomes) of non-photosynthetic plants generally undergoes gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequenced and assembled the complete plastomes of three holoparasitic Cistanche species (C. salsa, C. tubulosa and C. sinensis) and compared them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences on entire plastome, long single copy region and non-coding region, and different patterns of the retention/loss of functional genes. With few exception of putatively functional genes, massive plastid fragments which have been lost and transferred into the mitochondrial or nuclear genomes are nonfunctional. In contrast with the equivalents of the Orobanche species, some plastid-derived genes with diverse genomic locations are found in Cistanche. The early and initially diverged clades in different genera such as Cistanche and Aphyllon possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.