First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae).

Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes but not in Corylopsis. Plastid genomes of Corylopsis species (Corylopsis gotoana, Corylopsis pauciflora, and Corylopsis sinensis) were sequenced using next-generation sequencing techniques. Repeats and nucleotide diversity that could be used as DNA markers were also investigated. A phylogenetic investigation was carried out using 79 protein-coding genes to infer the evolutionary relationships within the genus Corylopsis. By including new plastomes, the overall plastid genome structure of Corylopsis was similar. Simple sequence repeats of 73-106 SSRs were identified in the protein-coding genes of the plastid genomes, and 33-40 long repeat sequences were identified in the plastomes. The Pi value of the rpl33_rps18 region, an intergenic spacer, was the highest. Phylogenetic analysis demonstrated that Corylopsis is a monophyletic group and Loropetalum is closely related to Corylopsis. C. pauciflora, C. gotoana, and C. spicata formed a clade distributed in Japan, whereas C. sinensis, C. glandulifera, and C. velutina formed a clade that was distributed in China.

Characteristics of chloroplast and mitochondrial genomes and intracellular gene transfer in the Korean endemic shrub, Sophora koreensis Nakai (Fabaceae).

Sophora koreensis Nakai, an endemic species distributed only in the Korean Peninsula, is of great geographical, economic, and taxonomic importance. Although its complete chloroplast (cp) genome sequence has been reported, its mitochondrial (mt) genome sequence has not yet been studied. Therefore, in this study, we aimed to investigate its mt genome sequence and compare it with those reported for other Fabaceae species. Total genomic DNA was extracted from fresh S. koreensis leaves collected from natural habitats in Gangwon-do Province, South Korea. This was followed by polymerase chain reaction (PCR) amplification of cpDNA insertions in the mt genome and the detection of microsatellites and dispersed repeats in the cp and mt genomes. Finally, the cp and mt genomes of S. koreensis were compared with those reported for other Fabaceae species. The cp sequence of S. koreensis showed identical gene orders and contents as those previously reported. Only six substitutions and one deletion were detected with 99 % homology. Conversely, the complete mt genome sequence, which was 517,845 bp in length and encoded 61 genes, including 43 protein-coding, 15 transfer RNAs, and 3 ribosomal RNA genes, was considerably different from that of S. japonica in terms of gene order and composition. Further, the mt genome of S. koreensis included ca. 7 and 3 kb insertions, representing an intracellular gene transfer (IGT) event, and the regions with these insertions were determined to be originally present in the cp genome. This IGT event was also confirmed via PCR amplification. IGT events can be induced via biological gene expression control or the use of repetitive sequences, and they provide important insights into the evolutionary lineage of S. koreensis. However, further studies are needed to clarify the gene transfer mechanisms between the two organelles.

Characterization of the complete plastid genome and phylogenetic implication of Micranthes octopetala (Nakai) Y.I.Kim & Y.D.Kim (Saxifragaceae), endemic to Korea.

Micranthes octopetala (Nakai) Y.I.Kim & Y.D. Kim et al. 2015, which belongs to the family Saxifragaceae, is a perennial herb endemic to Korea. M. octopetala was originally treated as a synonym of M. manchuriensis. However, in 2015, molecular phylogenetic analysis confirmed that M. octopetala is an independent species. In this study, the plastid genome of M. octopetala was sequenced for the first time, and the taxonomic position of this species was identified. The complete plastid genome of M. octopetala has a total length of 149 751 bp (large single copy: 83 083 bp; small single copy: 17 196 bp; inverted repeat: 24 736 bp), containing 130 genes, including 79 CDS, 30 tRNAs, and 4 rRNAs. Moreover, the absence of intron in the rpl2 gene, which is a common feature of Saxifragaceae, was confirmed. Phylogenetic analysis based on 79 protein-coding genes from 21 species revealed that M. octopetala belongs to the genus Micranthes, being a sister to other Micranthes species. The plastid genome of M. octopetala obtained in this study provides fundamental information for future studies on the genus Micranthes.

Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome.

Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.

First record of the complete chloroplast genome of Polygonatum infundiflorum (Asparagaceae), a Korean endemic species.

Polygonatum infundiflorum Y.S. Kim, B.U. Oh & C.G. Jang et al. 1998 is a Korean endemic species. This is first report on the complete chloroplast genome sequence of P. infundiflorum. The complete chloroplast genome length was 154,578 bp with a GC content of 37.7%. The large single-copy (LSC) region was 83,527 bp long, and the small single-copy (SSC) region was 18,457 bp long. The paired inverted repeats (IRs) were 26,297 bp and separated the LCS and SSC regions. There were 113 genes, comprising 78 protein-coding genes, four rRNA genes, 30 tRNA genes, and one pseudogene (infA). In total, 16 genes contained one intron, and two genes contained two introns. Phylogenetic analysis suggested that Polygonatum was divided into three sections, each forming a monophyletic group. P. infundiflorum was sister to P. macropodum and formed a monophyletic group with P. inflatum. This study provides basic information for future research and contributes to taxonomic and genetic studies on Polygonatum.

Complete plastid genome of Lespedeza tricolor (Fabaceae), an endemic shrub in Korea.

Lespedeza tricolor is a species found in the southern province of Korea, thought to be endemic to Korea. The complete plastid genome of this legume was sequenced in this study. DNA from L. tricolor was extracted, sequenced, and assembled into the complete plastid genome. We used 18 species of the family Fabaceae and 77 protein-coding genes to perform phylogenetic analysis. The plastid genome is 149,038 bp in length, with large (82,495 bp) and small (18,889 bp) single-copy regions, separated by a pair of inverted repeat regions (23,827 bp). It contains 83 protein-coding genes, eight rRNAs, 37 tRNAs, and two pseudogenes (rpl22 and infA). Our phylogenetic analysis suggests that the genus Lespedeza is monophyletic and L. tricolor is closely related to L. maritima and L. buergeri. In this study, we identified the phylogenetic position of L. tricolor and provided the data that can be used in various ways in future studies.

First record of the complete chloroplast genome of Syneilesis aconitifolia (Asteraceae).

Syneilesis aconitifolia is an herbaceous perennial of the Asteraceae family native to forests in China, Korea, Japan, and eastern Russia. In Korea, the young leaves of the plant are edible and the extract is known to have antitumor effects. The length of the complete plastome was found to be 150,773 bp, including 130 genes, consisting of 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The assembled plastome showed typical structure and gene content of the angiosperm plastome, which includes two inverted repeats (IR) regions of 24839 bp, a large single copy (LSC) region of 82911 bp, and a small single-copy (SSC) region of 18184 bp. The total G/C content in the S. aconitifolia plastome was 37.5%. The maximum likelihood (ML) phylogenetic tree strongly supports that S. aconitifolia is closely related to the hosts of Ligularia fischeri. This study reports the first complete chloroplast genome of the genus Syneilesis and will contribute to the phylogenetics of the family Asteraceae.

Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing.

This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.

Complete chloroplast genome of Clematis taeguensis (Ranunculaceae), an endemic species from South Korea.

The complete chloroplast (cp) genome sequence of Clematis taeguensis Y.N.Lee (Ranunculaceae) was determined to be 159,534 bp in length, consisting of large (79,326 bp) and small (18,338 bp) single-copy regions and a pair of identical inverted repeats (30,935 bp). The genome contains 92 protein-coding genes, 32 tRNA genes, 8 rRNA genes, and 1 pseudogene (infA). Phylogenetic analysis of 19 taxa inferred from the chloroplast genome showed a relationship with C. taeguensis, which is also recognized as a species endemic to the Korean Peninsula. The complete cp genome sequence of C. taeguensis reported here provides important information for future phylogenetic and evolutionary studies in Ranunculaceae.

Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates.

Previous studies on the chloroplast genome in Clematis focused on the chloroplast structure within Anemoneae. The chloroplast genomes of Cleamtis were sequenced to provide information for studies on phylogeny and evolution. Two Korean endemic Clematis chloroplast genomes (Clematis brachyura and C. trichotoma) range from 159,170 to 159,532 bp, containing 134 identical genes. Comparing the coding and non-coding regions among 12 Clematis species revealed divergent sites, with carination occurring in the petD-rpoA region. Comparing other Clematis chloroplast genomes suggested that Clematis has two inversions (trnH-rps16 and rps4), reposition (trnL-ndhC), and inverted repeat (IR) region expansion. For phylogenetic analysis, 71 protein-coding genes were aligned from 36 Ranunculaceae chloroplast genomes. Anemoneae (Anemoclema, Pulsatilla, Anemone, and Clematis) clades were monophyletic and well-supported by the bootstrap value (100%). Based on 70 chloroplast protein-coding genes, we compared nonsynonymous (dN) and synonymous (dS) substitution rates among Clematis, Anemoneae (excluding Clematis), and other Ranunculaceae species. The average synonymoussubstitution rates (dS)of large single copy (LSC), small single copy (SSC), and IR genes in Anemoneae and Clematis were significantly higher than those of other Ranunculaceae species, but not the nonsynonymous substitution rates (dN). This study provides fundamental information on plastid genome evolution in the Ranunculaceae.

Genetic Admixture in the Population of Wild Apple (Malus Sieversii) from the Tien Shan Mountains, Kazakhstan.

There is growing attention given to gene flow between crops and the wild relatives as global landscapes have been rapidly converted into agricultural farm fields over the past century. Crop-to-wild introgression may advance the extinction risks of rare plants through demographic swamping and/or genetic swamping. Malus sieversii, the progenitor of the apple, is exclusively distributed along the Tien Shan mountains. Habitat fragmentation and hybridization between M. sieversii and the cultivated apples have been proposed to be the causal mechanism of the accelerated extinction risk. We examined the genetic diversity pattern of eleven wild and domesticated apple populations and assessed the gene flow between M. sieversii and the cultivated apples in Kazakhstan using thirteen nuclear microsatellite loci. On average, apple populations harbored fairly high within-population diversity, whereas population divergences were very low suggesting likely influence of human-mediated dispersal. Assignment results showed a split pattern between the cultivated and wild apples and frequent admixture among the apple populations. Coupled with the inflated contemporary migration rates, the admixture pattern might be the signature of increased human intervention within the recent past. Our study highlighted the prevalent crop to wild gene flow of apples occurring in Kazakhstan, proposing an accelerated risk of genetic swamping.

First report of complete chloroplast genome sequence of monotypic genus Astilboides (Saxifragaceae) in North East Asia.

The complete chloroplast genome sequence of Astilboides tabularis, one of endemic species of Eastern Asia, was determined. The chloroplast genome was 157,147 bp in length with large single-copy (87,703 bp), small single-copy (18,268 bp) and a pair of inverted repeats (25,588 bp). In total, 131 genes were encoded, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis using concatenated 77 protein-coding genes of 15 species chloroplast genome revealed that A. tabularis was sister to the clade containing Bergenia, Oresitrophe, and Mukdenia.

The complete chloroplast genome sequence of Liparis yongnoana, an endemic orchid of Korea.

The complete chloroplast genome sequence of Liparis yongnoana was determined and analyzed in this study. The chloroplast genome size is 153,165 bp in length with 36.9% GC content. It comprises a large single-copy region (LSC) of 83,690 bp, a small single copy region (SSC) of 17,661 bp, and a pair of inverted repeat regions (IRa and IRb) of 25,907 bp separated by the SSC. The genome contains 132 genes, including 86 protein-coding, eight ribosomal RNA, and 38 transfer RNA genes. Phylogenetic analysis inferred from 16 Orchidaceae chloroplast genomes suggested that L. yongnoana was closely related to L. loeselii.

The mitochondrial genome of a social wasp, Vespa simillima simillima (Hymenoptera: Vespidae).

We analyzed the complete mitochondrial genome of a social wasp, Vespa simillima simillima from South Korea prior to a systematic study on Korean Vespidae. The mitogenome is 16,740 bp in length, includes 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a 228 bp short A + T-rich region. The overall base composition is 82.0% AT and 18.0% GC. The maximum-likelihood analysis suggested that V. s. simillima is closely related to V. bicolor, another species of Vespidae.

Molecular Phylogeny and Dating of Forsythieae (Oleaceae) Provide Insight into the Miocene History of Eurasian Temperate Shrubs.

Tribe Forsythieae (Oleaceae), containing two genera (Abeliophyllum and Forsythia) and 13 species, is economically important plants used as ornamentals and in traditional medicine. This tribe species occur primarily in mountainous regions of Eurasia with the highest species diversity in East Asia. Here, we examine 11 complete chloroplast genome and nuclear cycloidea2 (cyc2) DNA sequences of 10 Forsythia species and Abeliophyllum distichum using Illumina platform to provide the phylogeny and biogeographic history of the tribe. The chloroplast genomes of the 11 Forsythieae species are highly conserved, except for a deletion of about 400 bp in the accD-psaI region detected only in Abeliophyllum. Within Forsythieae species, analysis of repetitive sequences revealed a total of 51 repeats comprising 26 forward repeats, 22 palindromic repeats, and 3 reverse repeats. Of those, 19 repeats were common and 32 were unique to one or more Forsythieae species. Our phylogenetic analyses supported the monophyly of Forsythia and its sister group is Abeliophyllum using the concatenated dataset of 78 chloroplast genes. Within Forsythia, Forsythia likiangensis and F. giraldiana were basal lineages followed by F. europaea; the three species are characterized by minutely serrate or entire leaf margins. The remaining species, which are distributed in East Asia, formed two major clades. One clade included F. ovata, F. velutina, and F. japonica; they are morphologically supported by broadly ovate leaves. Another clade of F. suspensa, F. saxatilis, F. viridissima, and F. koreana characterized by lanceolate leaves (except F. suspensa which have broad ovate leaves). Although cyc2 phylogeny is largely congruent to chloroplast genome phylogeny, we find the discordance between two phylogenies in the position of F. ovata suggesting that introgression of the chloroplast genome from one species into the nuclear background of another by interspecific hybridization in East Asian Forsythia species. Molecular dating and biogeographic reconstructions suggest an origin of the Forsythieae species in East China in the Miocene. Distribution patterns in Forsythia indicated that the species were radially differentiated from East China, and the speciation of the European F. europaea was the result of both vicariance and dispersal in the late Miocene to Pliocene.

Characterization of complete chloroplast genome of endemic species of Korea Peninsular, Salvia chanryoenica (Lamiaceae).

Salvia chanryoenica is an endemic species, which locates on the ridges of mountains in South Korea. In this study, we determined the complete chloroplast (cp) genome sequence of S. chanryoenica; cp genome of S. chanryoenica is 151,689 bp in length and consists of a large (82,903 bp) and small (17,634 bp) single-copy regions, separated by a pair of identical inverted repeats (25,576 bp). This genome contains unique 79 protein-coding genes, 30 tRNA, and 4 rRNA. The gene order and organization of the S. chanryoenica are consistent with those of other Lamiaceae cp genomes. The overall GC content of the whole genome was 37.9%. Phylogenetic tree constructed based on 71 protein-coding genes demonstrated a sister relationship within genus Salvia.