Kyoung Su Choi

The Complete Chloroplast Genome Sequences of Three Veroniceae Species (Plantaginaceae): Comparative Analysis and Highly Divergent Regions

Previous studies of Veronica and related genera were weakly supported by molecular and paraphyletic taxa. Here, we report the complete chloroplast genome sequence of Veronica nakaiana and the related species Veronica persica and Veronicastrum sibiricum. The chloroplast genome length of V. nakaiana, V. persica, and V. sibiricum ranged from 150,198 bp to 152,930 bp. A total of 112 genes comprising 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes were observed in three chloroplast genomes. The total number of SSRs was 48, 51, and 53 in V. nakaiana, V. persica, and V. sibiricum, respectively. Two SSRs (10 bp of AT and 12 bp of AATA) were observed in the same regions (rpoC2 and ndhD) in three chloroplast genomes. A comparison of coding genes and non-coding regions between V. nakaiana and V. persica revealed divergent sites, with the greatest variation occurring petD-rpoA region. The complete chloroplast genome sequence information regarding the three Veroniceae will be helpful for elucidating Veroniceae phylogenetic relationships.

The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae); genomic features and relationship with Asteraceae.

Aster spathulifolius, a member of the Asteraceae family, is distributed along the coast of Japan and Korea. This plant is used for medicinal and ornamental purposes. The complete chloroplast (cp) genome of A. sphathulifolius consists of 149,473 bp that include a pair of inverted repeats of 24,751 bp separated by a large single copy region of 81,998 bp and a small single copy region of 17,973 bp. The chloroplast genome contains 78 coding genes, four rRNA genes and 29 tRNA genes. When compared to other cpDNA sequences of Asteraceae, A. spathulifolius showed the closest relationship with Jacobaea vulgaris, and its atpB gene was found to be a pseudogene, unlike J. vulgaris. Furthermore, evaluation of the gene compositions of J. vulgaris, Helianthus annuus, Guizotia abyssinica and A. spathulifolius revealed that 13.6-kb showed inversion from ndhF to rps15, unlike Lactuca of Asteraceae. Comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates with J. vulgaris revealed that synonymous genes related to a small subunit of the ribosome showed the highest value (0.1558), while nonsynonymous rates of genes related to ATP synthase genes were highest (0.0118). These findings revealed that substitution has occurred at similar rates in most genes, and the substitution rates suggested that most genes is a purified selection.

The Chloroplast Genome of Elaeagnus macrophylla and trnH Duplication Event in Elaeagnaceae.

Elaeagnaceae, which harbor nitrogen-fixing actinomycetes, is a plant family of the Rosales and sister to Rhamnaceae, Barbeyaceae and Dirachmaceae. The results of previous molecular studies have not strongly supported the families of Elaeagnaceae, Rhamnaceae, Barbeyaceae and Dirachmaceae. However, chloroplast genome studies provide valuable phylogenetic information; therefore, we determined the chloroplast genome of Elaeaganus macrophylla and compared it to that of Rosales such as IR junction and infA gene. The chloroplast genome of Elaeagnus macrophylla is 152,224 bp in length and the infA gene of E. macrophylla was psuedogenation. Phylogenetic analyses based on 79 genes in 30 species revealed that Elaeagnus was closely related to Morus. Comparison of the IR junction in six other rosids revealed that the trnH gene contained the LSC region, whereas E. macrophylla contained a trnH gene duplication in the IR region. Comparison of the LSC/IRb (JLB) and the IRa/LSC (JLA) regions of Elaeagnaceae (Elaeagnus and Shephedia) and Rhamnaceae (Rhamnus) showed that trnH gene duplication only occurred in the Elaeagnaceae. The complete chloroplast genome of Elaeagnus macrophylla provides unique characteristics in rosids. The infA gene has been lost or transferred to the nucleus in rosids, while E. macrophylla lost the infA gene. Evaluation of the chloroplast genome of Elaeagnus revealed trnH gene duplication for the first time in rosids. The availability of Elaeagnus cp genomes provides valuable information describing the relationship of Elaeagnaceae, Barbeyaceae and Dirachmaceae, IR junction that will be valuable to future systematics studies.

Phylogenetic Relationships of the Fern Cyrtomium falcatum (Dryopteridaceae) from Dokdo Island Based on Chloroplast Genome Sequencing

Cyrtomium falcatum is a popular ornamental fern cultivated worldwide. Native to the Korean Peninsula, Japan, and Dokdo Island in the Sea of Japan, it is the only fern present on Dokdo Island. We isolated and characterized the chloroplast (cp) genome of C. falcatum, and compared it with those of closely related species. The genes trnV-GAC and trnV-GAU were found to be present within the cp genome of C. falcatum, whereas trnP-GGG and rpl21 were lacking. Moreover, cp genomes of Cyrtomium devexiscapulae and Adiantum capillus-veneris lack trnP-GGG and rpl21, suggesting these are not conserved among angiosperm cp genomes. The deletion of trnR-UCG, trnR-CCG, and trnSeC in the cp genomes of C. falcatum and other eupolypod ferns indicates these genes are restricted to tree ferns, non-core leptosporangiates, and basal ferns. The C. falcatum cp genome also encoded ndhF and rps7, with GUG start codons that were only conserved in polypod ferns, and it shares two significant inversions with other ferns, including a minor inversion of the trnD-GUC region and an approximate 3 kb inversion of the trnG-trnT region. Phylogenetic analyses showed that Equisetum was found to be a sister clade to Psilotales-Ophioglossales with a 100% bootstrap (BS) value. The sister relationship between Pteridaceae and eupolypods was also strongly supported by a 100% BS, but Bayesian molecular clock analyses suggested that C. falcatum diversified in the mid-Paleogene period (45.15 ± 4.93 million years ago) and might have moved from Eurasia to Dokdo Island.

Genetic Diversity and Differentiation of a Narrowly Distributed and Endemic Species, Aster spathulifolius Maxim (Asteraceae), Revealed with Inter Simple Sequence Repeat Markers

Aster spathulifolius Maxim is a narrowly distributed and endemic species occurring in coastal regions of Korea and Japan. The genetic diversity and differentiation of fifteen populations of the species were analyzed in eight-two loci using six Inter Simple Sequence Repeat primers. Total genetic diversity at species level was extremely high (P=98.78%, Hsp=0.333±0.144, I=0.501±0.180), whereas the genetic diversity at population level was relatively low (P=43.74%, Hpop=0.150±0.189, I=0.227±0.274). High genetic differentiation among populations was detected based on genetic differentiation coefficient (Gst=0.549) and analysis of molecular variance (AP=54.06%). These findings together with low gene flow estimates (Nm=0.205) suggest that genetic drift by isolation is the most critical factor for establishing the current genetic structure of the species. The decrease in abundance of A. spathulifolius along with low levels of genetic diversity indicates that conservation strategies are necessary.

The Vascular Plants in Mt. Bohyeon, Gyeongbuk, Korea

This study was carried out to investigate the vascular plants of Mt. Bohyeon (Gyeongbuk). The vascular plants were collected 22 times and summarized as 589 taxa, including 105 families, 327 genera, 522 species, 11 subspecies, 48 varieties and 8 forms respectively. Among them, 13 Korean endemics, 10 red list of vascular plants, 2 endangered plants and 83 specially designated plants by the Ministry of Environment were included respectively. The naturalized plants were 37 taxa and the naturalized ratio was 6.41 of 589 taxa. Usage of 589 taxa were consists of 240 taxa (40.1%) of edible plants, 205 taxa (34.2%) of medicinal plants, 62 taxa (10.3%) of ornamental plants, 213 taxa (35.6%) of pasture plants, 15 taxa (2.5%) of timber plants, 8 taxa (1.3%) of fiberplants, and 3 taxa (0.5%) of industrial plants.

The complete chloroplast genome sequence of Euonymus japonicus (Celastraceae).

Abstract The complete chloroplast (cp) genome sequence of the Euonymus japonicus, the first sequenced of the genus Euonymus, was reported in this study. The total length was 157 637 bp, containing a pair of 26 678 bp inverted repeat region (IR), which were separated by small single copy (SSC) region and large single copy (LSC) region of 18 340 bp and 85 941 bp, respectively. This genome contains 107 unique genes, including 74 coding genes, four rRNA genes, and 29 tRNA genes. Seventeen genes contain intron of E. japonicus, of which three genes (clpP, ycf3, and rps12) include two introns. The maximum likelihood (ML) phylogenetic analysis revealed that E. japonicus was closely related to Manihot and Populus.

The complete chloroplast genome sequence of the Korean endemic plant Scrophularia takesimensis

Abstract The chloroplast genome sequence of Scrophularia takesimensis (Scrophulariaceae) was determined in this study. The cpDNA was 152,425 bp in length, containing a pair of 25,478 bp inverted repeat regions (IR), which were separated by small and large single copy region (SSC and LSC) of 17,938 bp and 83,531 bp, respectively. There are total of 113 genes in the genome, including 79 protein coding genes, 29 tRNA genes, 4 rRNA genes. 18 genes encoded one or two introns. The overall AT contents of the cpDNA were 61.9% and in the LSC, SSC and IR regions were 63.8%, 67.8% and 56.8%, respectively.

Complete chloroplast genome of Tetragonia tetragonioides: Molecular phylogenetic relationships and evolution in Caryophyllales

The chloroplast genome of Tetragonia tetragonioides (Aizoaceae; Caryophyllales) was sequenced to provide information for studies on phylogeny and evolution within Caryophyllales. The chloroplast genome of Tetragonia tetragonioides is 149,506 bp in length and includes a pair of inverted repeats (IRs) of 24,769 bp that separate a large single copy (LSC) region of 82,780 bp and a small single copy (SSC) region of 17,188 bp. Comparative analysis of the chloroplast genome showed that Caryphyllales species have lost many genes. In particular, the rpl2 intron and infA gene were not found in T. tetragonioides, and core Caryophyllales lack the rpl2 intron. Phylogenetic analyses were conducted using 55 genes in 16 complete chloroplast genomes. Caryophyllales was found to divide into two clades; core Caryophyllales and noncore Caryophyllales. The genus Tetragonia is closely related to Mesembryanthemum. Comparisons of the synonymous (Ks), nonsynonymous (Ka), and Ka/Ks substitution rates revealed that nonsynonymous substitution rates were lower than synonymous substitution rates and that Ka/Ks rates were less than 1. The findings of the present study suggest that most genes are a purified selection.

The Chloroplast Genome of Symplocarpus renifolius: A Comparison of Chloroplast Genome Structure in Araceae

Symplocarpus renifolius is a member of Araceae family that is extraordinarily diverse in appearance. Previous studies on chloroplast genomes in Araceae were focused on duckweeds (Lemnoideae) and root crops (Colocasia, commonly known as taro). Here, we determined the chloroplast genome of Symplocarpus renifolius and compared the factors, such as genes and inverted repeat (IR) junctions and performed phylogenetic analysis using other Araceae species. The chloroplast genome of S. renifolius is 158,521 bp and includes 113 genes. A comparison among the Araceae chloroplast genomes showed that infA in Lemna, Spirodela, Wolffiella, Wolffia, Dieffenbachia and Colocasia has been lost or has become a pseudogene and has only been retained in Symplocarpus. In the Araceae chloroplast DNA (cpDNA), psbZ is retained. However, psbZ duplication occurred in Wolffia species and tandem repeats were noted around the duplication regions. A comparison of the IR junction in Araceae species revealed the presence of ycf1 and rps15 in the small single copy region, whereas duckweed species contained ycf1 and rps15 in the IR region. The phylogenetic analyses of the chloroplast genomes revealed that Symplocarpus are a basal group and are sister to the other Araceae species. Consequently, infA deletion or pseudogene events in Araceae occurred after the divergence of Symplocarpus and aquatic plants (duckweeds) in Araceae and duplication events of rps15 and ycf1 occurred in the IR region.