Mitochondrial genome evolution in the orchid subfamily Cypripedioideae (Orchidaceae)

In this study, the mitogenomes of nine species in the subfamily Cypripedioideae were newly sequenced and assembled using both short and long reads for evolutionary analyses. Complete multi-chromosomal mitogenomes were obtained for Cypripedium subtropicum, C. henryi, Phragmipedium humboldtii, Phr. kovachii, and Paphiopedilum micranthum, and draft assemblies were obtained for four additional Paphiopedilum species. Thirty-nine protein-coding genes were annotated and shared in nine sampled species. sdh4 was discovered in all species of Cypripedioideae, and rpl10 was detected in four species of Paphiopedilum. These two genes might have been horizontally transferred from non-orchid plants at different times. Approximately 101 to 998 repeat sequences were identified with total lengths of 417,136 to 785,960 bp in the mitogenomes of Cypripedioideae. There were 634 and 662 RNA editing sites in C. subtropicum and Pa. gratrixianum, respectively, and C-to-U editing was dominant. The nad and ccm genes exhibited high frequencies of RNA editing. Our study revealed the complexity of orchid mitogenomes, including evidence for the horizontal transfer of rpl10 and sdh4.