The genus Lilium L. is widely distributed in the cold and temperate regions of the Northern Hemisphere and is one of the most valuable plant groups in the world. Regarding the classification of the genus Lilium, Comber’s sectional classification, based on the natural characteristics, has been primarily used to recognize species and circumscribe the sections within the genus. Although molecular phylogenetic approaches have been attempted using different markers to elucidate their phylogenetic relationships, there still are unresolved clades within the genus. In this study, we constructed the species tree for the genus using 28 Lilium species plastomes, including three currently determined species (L. candidum, L. formosanum, and L. leichtlinii var. maximowiczii). We also sought to verify Comber’s classification and to evaluate all loci for phylogenetic molecular markers. Based on the results, the genus was divided into two major lineages, group A and B, consisting of eastern Asia + Europe species and Hengduan Mountains + North America species, respectively. Sectional relationships revealed that the ancestor Martagon diverged from Sinomartagon species and that Pseudolirium and Leucolirion are polyphyletic. Out of all loci in that Lilium plastome, ycf1, trnF-ndhJ, and trnT-psbD regions are suggested as evaluated markers with high coincidence with the species tree. We also discussed the biogeographical diversification and long-distance dispersal event of the genus.

In this study, four plastomes of Hymenophyllum, distributed in the Korean peninsula, were newly sequenced and phylogenomic analysis was conducted to reveal (1) the evolutionary history of plastomes of early-diverging fern species at the species level, (2) the importance of mobile open reading frames in the genus, and (3) plastome sequence divergence providing support for H. coreanum to be recognized as an independent species distinct from H. polyanthos. In addition, 1C-values of H. polyanthos and H. coreanum were measured to compare the genome size of both species and to confirm the diversification between them. The rrn16-trnV intergenic regions in the genus varied in length caused by Mobile Open Reading Frames in Fern Organelles (MORFFO). We investigated enlarged noncoding regions containing MORFFO throughout the fern plastomes and found that they were strongly associated with tRNA genes or palindromic elements. Sequence identity between plastomes of H. polyanthos and H. coreanum is quite low at 93.35% in the whole sequence and 98.13% even if the variation in trnV-rrn16 intergenic spacer was ignored. In addition, different genome sizes were found for these species based on the 1C-value. Consequently, there is no reason to consider them as a conspecies.

It is very important to confirm and understand the genetic background of cultivated plants used in multiple applications. The genetic background is the history of crossing between maternal and paternal plants to generate a cultivated plant. If the plant in question was generated from a simple origin and not complicated crossing, we can easily confirm the history using a phylogenetic tree based on molecular data. This study was conducted to trace the origin of “Tottori Fujita 1gou” and “Tottori Fujita 2gou”, which are registered as cultivars originating from Phedimus kamtschaticus. To investigate the phylogenetic position of these cultivars, the backbone tree of the genus Phedimus needed to be further constructed because it retains inarticulate phylogenetic relationships among the wild species. We performed molecular phylogenetic analysis for P. kamtschaticus, Phedimus takesimensis, Phedimus aizoon, and Phedimus middendorffianus, which are assumed as the species of origin for “Tottori Fujita 1gou” and “Tottori Fujita 2gou”. The molecular phylogenetic tree based on the internal transcribed spacer (ITS) and psbA-trnH sequences showed the monophyly of the genus Phedimus, with P. takesimensis forming a single clade. However, P. kamtschaticus and P. aizoon were scattered in the tree. It was verified that “Tottori Fujita 1gou” and “Tottori Fujita 2gou” were embedded in a clade with P. takesimensis and not P. kamtschaticus. Therefore, origination from P. takesimensis was strongly supported. Based on these results, molecular phylogenetic analysis is suggested as a powerful tool for clearly tracing the origin of cultivated plants.

Fern gametophytes have often been neglected in research; however, studies on gametophytes are crucial for a better understanding of the evolution of ferns. During their life cycle, some gametophytes produce large and long‐lived populations without producing sporophytes and reproduce independently through asexual means, such as through the formation of gemmae. In this study, we investigated independent gametophytes on the Jeju Island of Korea, which was located on the land bridge between East China and Japan during the glacial periods. Fourteen gametophyte populations were collected from seven sites, of which 13 populations were clearly identified as belonging to four fern species known to occur in Jeju Island with BLAST searches using rbcL and trnL‐F sequences. Surprisingly, the last remaining population constituted undescribed taxa in Korea. We presented the first report of the independent gametophytes of Antrophyum obovatum Baker which has not been previously recorded in Korea. It has been supposed that many ferns sought suitable habitat throughout the land bridge between China and Japan. However, Jeju Island might be unsuitable for vittarioid ferns that prefer a tropical or subtropical environment. Consequently, only two species of vittariod ferns (A. obovatum and Haplopteris flexuosa (Fée) E.H. Crane) in the form of a gametophyte and sporophyte, respectively, exist on Jeju Island. Therefore, this gametophyte population must be protected and managed from a conservation perspective. In the case of the independent gametophyte of Hymenophyllum wrightii Bosch, haplotype analysis was conducted based on the rbcL sequences and the result supported that the North American populations were migrated from Japan through land bridge during the glacial periods and Jeju populations were recently established by long‐distance dispersal of the Japanese populations.

The complete chloroplast (cp) genome sequence of Ajania pacifica, called as golden and silver chrysanthemum, was newly analyzed in this study. It was 151,059 bp in length and was a typical circular structure composed of and comprised of a large single copy region (82,857 bp) and a small single copy region (18,294 bp) which were separated by two inverted repeat regions (24,954 bp). The molecular phylogenetic analyses of A. pacifica and its related taxa was conducted based on the complete chloroplast genome sequences, and it was proved that the genus Ajania is embedded in the genus Chrysanthemum clade as well as a monotypic genus Opisthopappus. In the other hand, the genus Artemisia was divided into two group in the tribe Anthemideae.

Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara is a broad-leaved valerian endemic to Ulleung Island, a noted hot spot of endemism in Korea. However, despite its widespread pharmacological use, this plant remains comparatively understudied. Plant cells generally contain two types of organellar genomes (the plastome and the mitogenome) that have undergone independent evolution, which accordingly can provide valuable information for elucidating the phylogenetic relationships and evolutionary histories of terrestrial plants. Moreover, the extensive mega-data available for plant genomes, particularly those of plastomes, can enable researchers to gain an in-depth understanding of the transfer of genes between different types of genomes. In this study, we analyzed two organellar genomes (the 155,179 bp plastome and the 1,187,459 bp mitogenome) of V. sambucifolia f. dageletiana and detected extensive changes throughout the plastome sequence, including rapid structural mutations associated with inverted repeat (IR) contraction and genetic variation. We also described features characterizing the first reported mitogenome sequence obtained for a plant in the order Dipsacales and confirmed frequent gene transfer in this mitogenome. We identified eight non-plastome-originated regions (NPRs) distributed within the plastome of this endemic plant, for six of which there were no corresponding sequences in the current nucleotide sequence databases. Indeed, one of these unidentified NPRs unexpectedly showed certain similarities to sequences from bony fish. Although this is ostensibly difficult to explain, we suggest that this surprising association may conceivably reflect the occurrence of gene transfer from a bony fish to the plastome of an ancestor of V. sambucifolia f. dageletiana mediated by either fungi or bacteria.