Highly Reduced Plastid Genomes of Non­-Photosynthetic Orchids Epipogium aphyllum and Epipogium roseum

Epipogium aphyllum and Epipogium roseum are orchids notable for multiple peculiar features such as non-photosynthetic lifestyle, unpredictable appearance and unusual floral morphology. Both species are rare and insufficiently studied, especially in their genetic aspects. Here we present the plastid genomes of Epipogium aphyllum and Epipogium roseum, which shed light on the genomic changes accompanying loss of photosynthetic ability. Plastid genomes were found to be highly reduced: with lengths of 30 kbp and 18 kbp, they are among the smallest plastid genomes known to date. They carry about 20% of protein-coding genes of a typical plant plastome. The retained genes are represented mainly by those encoding components of translation machinery, such as ribosomal RNA and proteins, transfer RNAs and a translation initiation factor. Also, two genes not related to translation – accD and clpP - are present. Reduction of plastid genomes is accompanied by multiple rearrangements and distortion of the typical plastid genome structure, which usually consists of two single copy regions interlaced with an inverted repeat. The plastid genomes show a significant increase in substitution rate. Sequencing of several samples of E. roseum reveals high protein sequence divergence (up to 20%), an extraordinary value for intraspecific comparisons. We hypothesize that the main reason for retention of plastid genomes in Epipogium, containing mostly genes of translation machinery, could be the necessity to translate mRNAs of accD and clpP which are significant for metabolism and not related to photosynthesis.