Origin and rapid evolution of minicircular and highly heteroplasmic mitogenome in the holoparasitic plant genus Rhopalocnemis

The holoparasitic plant Rhopalocnemis phalloides displays unique features in mitogenome organization, sequence heteroplasmy, DNA replication and gene transcription. To understand the origin and evolution of these unique features, we compared the mitogenomes of three R. phalloides individuals and one individual of a newly discovered congeneric species. These mitogenomes comprise dozens of minicircular chromosomes (∼2-8 kb), with fairly small mitogenome sizes between 121.1 and 147.5 kb. Each R. phalloides individual contains extremely conserved regions (CRs) on all chromosomes, yet these CRs vary significantly among individuals, suggesting rapid divergence in a concerted manner. In contrast, the congeneric species lacks such CRs. Although nearly identical gene and intron content, there is significant sequence divergence between the two species. Extremely high mitogenome heteroplasmy was observed in all three individuals of R. phalloides and all the variants of protein coding genes are transcribed, but few heteroplasmic variants are shared among the three individuals. No sequence heteroplasmy was detected in the congeneric species. PacBio sequencing revealed concatenated mitochondrial chromosomes in the two species, suggesting rolling circle replication of mitochondrial DNA. We infer that the origins of the CR and sequence heteroplasmy are later than the origin of all-minicircular chromosomes in Rhopalocnemis , and propose a plasmid incorporation model to explain the origin of the CR. The rapid intraspecific variation in mitogenome structure, sequence and heteroplasmy in R. phalloides may result from relaxed selective constraint. The striking heteroplasmy in the R. phalloides mitogenome can not be explained by mitochondrion-targeted DNA-RRR gene loss characterized in this study.