An unknown taxon of Stellaria was discovered in Yakushima, a Japanese island known to harbor several endemic species. To determine the identity of this taxon, this study employed MIG-seq for the reconstruction of a finely resolved phylogenetic tree of the newly discovered taxon, along with some related species of Stellaria. The results showed that the newly discovered taxon is a relative of S. alsine. Based on this result, Stellaria alsine subsp. nanasubsp. nov. was published.

Molecular phylogenetic studies of Hosta pulchella (Asparagaceae) and its relatives, which are native to Japan, have been conducted and resulted in a highly resolved phylogeny. Specifically, the relationship of H. pulchella to H. alata Hatusima, nom. nud. is investigated. These data include genome-wide SNPs obtained through conducting multiplexed ISSR genotyping by sequencing (MIG-seq). Based on these phylogenetic results, morphological observations, distribution, and differences in flowering periods of H. alata collections sympatric with H. pulchella, we find the two species closely related, but distinct. As such, we formally describe Hosta alatasp. nov. from the Oita Prefecture of Kyushu island, southwestern Japan.

According to the contemporary classification of Hydrangea native to Japan, H. serrata is a polymorphic species including six varieties. We discovered a plant identified as H. serrata, but morphologically distinct from previously known varieties, in Yakushima island where approximately 50 endemic species are known. To determine the relationship of this plant with previously known varieties, we examined morphology and constructed a highly resolved phylogeny of H. serrata and its relatives using three chloroplast genomic regions, rbcL, trnL intron, psbA-trnH, and two nuclear genomic regions, ITS1 and ITS2, and Multiplex ISSR genotyping by sequencing (MIG-seq). Based on these morphological and phylogenetic observations, we describe Hydrangea acuminata subsp. yakushimensissubsp. nov. as a newly discovered lineage in Yakushima, Japan and propose Hydrangea minamitaniistat. nov. and Hydrangea acuminata subsp. australisstat. nov. which were previously treated as varieties of H. serrata.

In May 2011, numerous poppy plants closely resembling Papaver bracteatum Lindl., a type of narcotic plant that is illegal in Japan, were distributed directly from several large flower shops or through online shopping throughout Japan, including the Tokyo Metropolitan area. In order to better identify the narcotic plants, the relative nuclear DNA content at the vegetative stage was measured by flow cytometric (FCM) analysis in 3 closely-related species of the genus Papaver section Oxytona, namely P. orientale, P. pseudo-orientale, and P. bracteatum, based on the difference between the chromosome numbers of these species. The results showed that the nuclear DNA content differed between these 3 species, and that most of the commercially distributed plants examined in this study could be identified as P. bracteatum. The remaining plants were P. pseudo-orientale, a non-narcotic plant. In addition, the FCM results for the identification of P. bracteatum completely agreed with the results obtained by the morphological analysis, the inter-genic spacer sequence of rpl16–rpl14 (PS-ID sequence) of chloroplast DNA, and the presence of thebaine. These results clearly indicate the usefulness of FCM analysis for the identification of P. bracteatum plants, including when they are in their vegetative stage.

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