The plastid genome of the non-photosynthetic plant Rhopalocnemis phalloides is one of the most polymorphic genomes known

Abstract

The common ancestor of plants in the Balanophoraceae family lost the ability to photosynthesize, and all several dozen extant species of this family feed exclusively by parasitizing other plants. Previous studies have shown that the plastid genomes of Balanophoraceae present numerous unusual features, including an extraordinarily increased rate of mutation accumulation without an observable weakening of natural selection acting on the genes. This study aims to test the hypothesis that the increased rate of mutation accumulation could have led to exceptionally high levels of intraspecific polymorphism in Balanophoraceae. To this end, we studied the plastid genomes of 7 samples of the species Rhopalocnemis phalloides. Although all 7 plastid genomes possessed the same genes arranged in the same order, the level of polymorphism was indeed extremely high, possibly the highest among all known genomes of any living organisms. Specifically, the average genome-wide percent identity of the plastid genomes of Rhopalocnemis phalloides was 68.7%, and the average percent identity of the CDSs was 68.9%. Additionally, during this study, we discovered 60 taxonomically misclassified plastid genomes in NCBI databases; this result has independent value.