Complete Plastid Genome of the Recent Holoparasite <i>Lathraea squamaria</i> Reveals Earliest Stages of Plastome Reduction in Orobanchaceae

<div><p>Plants from the family Orobanchaceae are widely used as a model to study different aspects of parasitic lifestyle including host–parasite interactions and physiological and genomic adaptations. Among the latter, the most prominent are those that occurred due to the loss of photosynthesis; they include the reduction of the photosynthesis-related gene set in both nuclear and plastid genomes. In Orobanchaceae, the transition to non-photosynthetic lifestyle occurred several times independently, but only one lineage has been in the focus of evolutionary studies. These studies included analysis of plastid genomes and transcriptomes and allowed the inference of patterns and mechanisms of genome reduction that are thought to be general for parasitic plants. Here we report the plastid genome of <i>Lathraea squamaria</i>, a holoparasitic plant from Orobanchaceae, clade Rhinantheae. We found that in this plant the degree of plastome reduction is the least among non-photosynthetic plants. Like other parasites, <i>Lathraea</i> possess a plastome with elevated absolute rate of nucleotide substitution. The only gene lost is <i>petL</i>, all other genes typical for the plastid genome are present, but some of them–those encoding photosystem components (22 genes), cytochrome b₆/f complex proteins (4 genes), plastid-encoded RNA polymerase subunits (2 genes), ribosomal proteins (2 genes), <i>ccsA</i> and <i>cemA</i>–are pseudogenized. Genes for cytochrome b₆/f complex and photosystems I and II that do not carry nonsense or frameshift mutations have an increased ratio of non-synonymous to synonymous substitution rates, indicating the relaxation of purifying selection. Our divergence time estimates showed that transition to holoparasitism in <i>Lathraea</i> lineage occurred relatively recently, whereas the holoparasitic lineage Orobancheae is about two times older.</p>