The largest plastome section in Orchidaceae: expanded size and large inversion of Cypripedium sect. Trigonopedia

The Cypripedium section Trigonopedium Franch is a medium sized group comprising eleven terrestrial perennial species with high ornamental and economic value. Here, I sequenced and assembled three plastomes of sect. Trigonopedia ( C. fargesii , C . sichuanense and C . lichiangense ) using a hybrid assembly method. The results showed the plastome sizes of sect. Trigonopedia were the largest in all sequenced samples of Orchidaceae to date and all expanded to more than 200 kb. The plastomes comprised of 112 unique genes with low GC content of 26-29.21% and C. lichiangense (234,657 bp) was the largest one in Orchidaceae and the second largest one in angiosperms so far. A large inversion (~ 80–90 kb) occurs from the trnG-UCC gene to trnP-UGG in LSC region in every plastome of the six expanded Cypripedium samples. AT-biased non-coding regions and more SSRs and larger repeats sequences were responsible for the expansion of the six enlarged plastomes. The whole set of ndh genes were intact and showed obviously more divergent than others. These findings may aid in the process in conservation and evolutionary research of the Orchidaceae.