Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Hydnora visseri (Hydnoraceae)

Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants are released from selective constraints due to the reduction or loss of photosynthetic ability. Their plastomes typically show decay in gene content and sometimes structure, too. Here, we present the small and highly divergent, yet functional plastome discovered in the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). While this ancient parasitic lineage has shifted from autotrophy to holoparasitism between 90 and 50 MY ago, its plastid genome has not been lost along the way. It has a size of 27 Kb, with just 24 genes encoding ribosomal proteins, ribosomal rRNAs, and housekeeping functions, but no genes related to photosynthesis. The inverted repeat and the small single copy regions have been tremendously reduced in size, each to ~1.5 Kb, and intergenic regions have almost been completely eliminated. Despite this extreme reduction, gene order and orientation is almost exactly collinear with the plastid genome of the closely related photosynthetic plant Piper cenocladum. Gene annotation was aided using several similarity-based search algorithms at the highest sensitivity levels possible. While open reading frames for these plastid genes are maintained, sequence similarity to orthologs in other plants is extremely low, presenting a substantial challenge for the detection and annotation of these genes. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long open reading frames with distant homology to other plastid genomes and a high genome copy number relative to the mitochondrial and nuclear genomes, suggests that the plastome remains functional.