The Largest Plastid Genome of Monocots: a Novel Genome Type Containing AT Residue Repeats in the Slipper Orchid Cypripedium japonicum

Plastid genome studies on Orchidaceae, one of the largest families of flowering plants, have been limited to the subfamily Epidendroideae. To increase understanding of the plastid genome evolution in Orchidaceae, we performed a complete plastid genome analysis of the slipper orchid Cypripedium japonicum positioned in the basal clade of the family. No significant gene deletions were observed in the plastid genome of the slipper orchid composed of 85 coding genes including members of the ndh gene family, which are mostly deleted or show pseudogenisation in orchids, although matK was identified as a pseudogene due to a frameshift mutation. Results also revealed that C. japonicum contains the largest plastid genome (174,417 bp) within monocots and the third largest one in Magnoliophyta. This is a new type of plastid genome extended due to abnormally frequent AT residue repeats within noncoding regions without inverted repeat (IR) expansion. In addition, we detected 25 plastid microsatellites and compared them among seven populations from Korea and Japan. These microsatellites may be applicable to population genetics and conservation biology studies on slipper orchids, which have become rare and are nearing extinction. AT-rich regions in the introns may also play a role in effective splicing of the genome after matK lost its function. As AT-rich regions are difficult to amplify and sequence using normal sequencing technologies, we propose a revised methodology for sequencing these regions.