Genetic diversification of Oberonia (Orchidaceae) in Japan

The purpose of our study is to clarify the classification and genetic differentiation of Japanese Oberonia. To clarify the genetic differentiation, we used multiplexed inter simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq), which can detect single-nucleotide polymorphisms (SNPs). 23 specimens of Oberonia from Honshu (Fukushima, Shizuoka), Shikoku (Kochi), Kyushu (Miyazaki), and the Ryukyus (Amami Island and Okinawa Island) were analyzed. Furthremore, to investigate the effect of different cycle numbers, the first PCR was performed at 25, 30, and 35 cycles. A phylogenetic tree was constructed using the MIG-seq SNPs data. The individual-based genetic structure was estimated using STRUCTURE 2.3.4 in the ipyrad analysis toolkit.