Publications by authors named "Myounghai Kwak"

37 Publications

The complete plastid genome sequence of (Fagaceae), an evergreen broad-leaved oak endemic to East Asia.

Mitochondrial DNA B Resour 2021 Feb 3;6(2):320-322. Epub 2021 Feb 3.

Department of Biology Education, Chonnam National University, Gwangju, Republic of Korea.

We are reporting the complete plastid genome (plastome) of , an evergreen broad-leaved oak endemic to East Asia. This species is important for maintaining the warm-temperate evergreen forest biome in East Asia. The plastome is 160,522 base pairs (bp) long, with two inverted repeat (IR) regions (25,839 bp each) that separate a large single copy (LSC) region (90,199 bp) and a small single copy (SSC) region (18,645 bp). The phylogenetic tree shows that is closely related to with strong bootstrap support.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2020.1866449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7872549PMC
February 2021

Three complete plastome sequences from the families of Lamiaceae, Mazaceae, and Phrymaceae (Lamiales).

Mitochondrial DNA B Resour 2021 Jan 19;6(1):224-226. Epub 2021 Jan 19.

Division of Life Sciences, Korea University, Seoul, South Korea.

In this study, we report the first complete plastome sequence of (Lamiaceae) (MT937186). In addition, the plastome sequences of subsp. (Phrymaceae) (153,324 bp; MT948145) and (Mazaceae) (152,847 bp; MT937187) are also included. The gene orders and structures of the three plastomes are collinear with those of the typical plastome of angiosperm. The plastome size of is 154,370 bp in length and consists of a large single-copy region of 85,079 bp and a small single-copy region of 17,917 bp, which are separated by a pair of 25,687 bp-long inverted repeat regions. In addition, the plastome sizes of subsp. and are 153,324 bp and 152,847 bp, respectively. The three plastomes contain 113 genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. Sixteen genes contain one intron and two genes have two introns. A total of 41 simple sequence repeat loci was identified in the plastome. Phylogenetic analysis shows that Viticoideae is a sister group of the last of Lamiaceae except Nepetoideae. The Mazaceae are a sister group of Lamiaceae, while Phrymaceae form a sister group to the Paulowniaceae-Orobanchaceae clade.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2020.1861563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7832541PMC
January 2021

The complete chloroplast genome of a Korean endemic species , Nakai.

Mitochondrial DNA B Resour 2020 Jul 29;5(3):3067-3068. Epub 2020 Jul 29.

Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea.

In this study, we report the complete chloroplast (cp) genome of and its relation with other species within the Fabaceae family. The cp genome was 154,870 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (25,866 bp) separated by a large (85,037 bp) and small (18,101 bp) single-copy (SC) region. The genome encodes a total of 84 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Phylogenetic analysis suggested that is closely related to genus within Fabaceae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2020.1797579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782127PMC
July 2020

The complete chloroplast genome of a fern genus .

Mitochondrial DNA B Resour 2020 Jan 14;5(1):572-573. Epub 2020 Jan 14.

Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea.

In this study, we report the complete chloroplast (cp) genome of , a fern member, and comparative analysis with its related family members. The cp genome was 155,983 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (25,614 bp) separated by a large (82,769 bp) and small (21,986 bp) single-copy (SC) region. The genome encodes a total of 88 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Additionally, we identified 86 RNA editing sites in 52 genes; most of the substitution was U to C (52 sites), while C to U conversion occurred in 34 positions. The phylogenetic analysis strongly supported the relationship of with and of Thelypteridoideae family.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2019.1710294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7748766PMC
January 2020

The complete chloroplast genome of a .

Mitochondrial DNA B Resour 2019 Dec 11;5(1):102-103. Epub 2019 Dec 11.

Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea.

is one of the diverse members of the fern group and medicinally important genus. In Korea, the natural resources of are being exhausted by excessive exploitation and require urgent conservation. In this study, the complete chloroplast genome of was generated, and its structure was compared with that of other members of same family. The chloroplast genome was 153224 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (24591 bp) separated by a large (82480 bp) and small (21562 bp) single-copy (SC) region. The genome encodes a total of 88 protein-coding genes, 35 tRNA genes, and eight rRNA genes. Additionally we identified 87 RNA editing sites in 52 genes; most of the substitution was U to C (50 sites), while C to U conversion occurred in 37 positions. The phylogenetic analysis strongly supported the relationship of with and. (Blechnoideae).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2019.1698366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7748671PMC
December 2019

Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae).

PLoS One 2020 26;15(10):e0241178. Epub 2020 Oct 26.

National Institute of Biological Resources, Incheon, Republic of Korea.

Iris is one of the largest genera in the family Iridaceae, comprising hundreds of species, including numerous economically important horticultural plants used in landscape gardening and herbal medicine. Improved taxonomic classification of Iris species, particularly the endangered Korean-native Iris, is needed for correct species delineation. To this end, identification of diverse genetic markers from Iris genomes would facilitate molecular identification and resolve ambiguous classifications from molecular analyses; however, only two Iris plastid genomes, from Iris gatesii and Iris sanguinea, have been sequenced. Here, we used high-throughput next-generation sequencing, combined with Sanger sequencing, to construct the plastid genomes of 14 Korean-native Iris species with one outgroup and predict their gene content. Using these data, combined with previously published plastid genomes from Iris and one outgroup (Sisyrinchium angustifolium), we constructed a Bayesian phylogenetic tree showing clear speciation among the samples. We further identified sub-genomic regions that have undergone neutral evolution and accurately recapitulate Bayesian-inferred speciation. These contain key markers that could be used to identify and classify Iris samples into taxonomic clades. Our results confirm previously reported speciation patterns and resolve questionable relationships within the Iris genus. These data also provide a valuable resource for studying genetic diversity and refining phylogenetic relationships between Iris species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241178PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7588056PMC
December 2020

A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak () in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization.

Genes (Basel) 2020 Sep 23;11(10). Epub 2020 Sep 23.

Department of Biology Education, Chonnam National University, Gwangju 61186, Korea.

Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. To test this hypothesis, we examined the levels of genetic diversity of marginal-edge populations of , restricted to a few habitats on Jeju Island, and compared them with the southern Kyushu populations. We also evaluated their evolutionary potential and conservation value. The genetic diversity and structure were analyzed using 40 polymorphic microsatellite markers developed in this study. Ecological Niche Modeling (ENM) has been employed to develop our insights, which can be inferred from historical distribution changes. Contrary to our expectations, we detected a similar level of genetic diversity in the Jeju populations, comparable to that of the southern Kyushu populations, which have been regarded as long-term glacial refugia with a high genetic variability of East Asian evergreen trees. We found no signatures of recent bottlenecks in the Jeju populations. The results of STRUCTURE, neighbor-joining phylogeny, and Principal Coordinate Analysis (PCoA) with a significant barrier clearly demonstrated that the Jeju and Kyushu regions are genetically distinct. However, ENM showed that the probability value for the distribution of the trees on Jeju Island during the Last Glacial Maximum (LGM) converge was zero. In consideration of these results, we hypothesize that independent massive postglacial colonization from a separate large genetic source, other than Kyushu, could have led to the current genetic diversity of Jeju Island. Therefore, we suggest that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU). These findings improve our understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11101114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7598624PMC
September 2020

Corrigendum: Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences.

Front Plant Sci 2020;11:322. Epub 2020 Mar 20.

Division of Life Sciences, Korea University, Seoul, South Korea.

[This corrects the article DOI: 10.3389/fpls.2020.00022.].
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2020.00322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099975PMC
March 2020

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences.

Front Plant Sci 2020 21;11:22. Epub 2020 Feb 21.

Division of Life Sciences, Korea University, Seoul, South Korea.

In order to understand the evolution of the orchid plastome, we annotated and compared 124 complete plastomes of Orchidaceae representing all the major lineages in their structures, gene contents, gene rearrangements, and IR contractions/expansions. Forty-two of these plastomes were generated from the corresponding author's laboratory, and 24 plastomes-including nine genera (, , , , , , , and )-are new in this study. All orchid plastomes, except and have a quadripartite structure consisting of a large single copy (LSC), two inverted repeats (IRs), and a small single copy (SSC) region. The IR region was completely lost in the plastomes. The SSC is lost in the plastome. The smallest plastome size was 19,047 bp, in and the largest plastome size was 178,131 bp, in . The small plastome sizes are primarily the result of gene losses associated with mycoheterotrophic habitats, while the large plastome sizes are due to the expansion of noncoding regions. The minimal number of common genes among orchid plastomes to maintain minimal plastome activity was 15, including the three subunits of (14, 16, and 36), seven subunits of (2, 3, 4, 7, 8, 11, and 14), three subunits of (5, 16, and 23), C-GCA, and P genes. Three stages of gene loss were observed among the orchid plastomes. The first was gene loss, which is widespread in Apostasioideae, Vanilloideae, Cypripedioideae, and Epidendroideae, but rare in the Orchidoideae. The second stage was the loss of photosynthetic genes (, and ) and gene subunits, which are restricted to and some species of and . The third stage was gene loss related to prokaryotic gene expression (, , and others), which was observed in , , and In addition, an intermediate stage between the second and third stage was observed in (Vanilloideae). The majority of intron losses are associated with the loss of their corresponding genes. In some orchid taxa, however, introns have been lost in 1616, and P(2) without their corresponding gene being lost. A total of 104 gene rearrangements were counted when comparing 116 orchid plastomes. Among them, many were concentrated near the IRa/b-SSC junction area. The plastome phylogeny of 124 orchid species confirmed the relationship of {Apostasioideae [Vanilloideae (Cypripedioideae (Orchidoideae, Epidendroideae))]} at the subfamily level and the phylogenetic relationships of 17 tribes were also established. Molecular clock analysis based on the whole plastome sequences suggested that Orchidaceae diverged from its sister family 99.2 mya, and the estimated divergence times of five subfamilies are as follows: Apostasioideae (79.91 mya), Vanilloideae (69.84 mya), Cypripedioideae (64.97 mya), Orchidoideae (59.16 mya), and Epidendroideae (59.16 mya). We also released the first nuclear ribosomal (nr) DNA unit (18S-ITS1-5.8S-ITS2-28S-NTS-ETS) sequences for the 42 species of Orchidaceae. Finally, the phylogenetic tree based on the nrDNA unit sequences is compared to the tree based on the 42 identical plastome sequences, and the differences between the two datasets are discussed in this paper.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2020.00022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7047749PMC
February 2020

Neuroprotective effects of Dendropanax morbifera leaves on glutamate-induced oxidative cell death in HT22 mouse hippocampal neuronal cells.

J Ethnopharmacol 2020 Apr 26;251:112518. Epub 2019 Dec 26.

College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, 16499, Republic of Korea. Electronic address:

Ethnopharmacological Relevance: Dendropanax morbifera (DM) has long been used as a traditional herbal medicine for migraines. Glutamate toxicity and oxidative stress have emerged as the possible triggers implicated in migraine pathogenesis.

Aim Of The Study: We aimed to examine the neuroprotective effects of DM leaves (DML) on glutamate-induced oxidative cell death in HT22 mouse hippocampal neuronal cells.

Materials And Methods: Molecular authentication of DML was assessed using DNA barcoding analysis. Four different solvent extracts of DML were prepared and subjected to antioxidant activity and phytochemical assays. Neuroprotective effects of DML extracts were evaluated using relevant biochemical and imaging assays that measure cell viability/death, ROS generation, Ca levels, mitochondrial dysfunction, and AIF nuclear translocation.

Results: The sequences of matK, rbcL, atpF-H, and psbK-I in DML were identical with those in voucher specimens, confirming that DML was indeed D. morbifera. The ethyl acetate extract of DML (DMLE) showed the highest flavonoid and phenolic content, and prominent DPPH/superoxide radical scavenging and reducing power activities. In the HT22 cell model, glutamate was shown to be the causative agent for apoptotic cell death via elevation of intracellular ROS and Ca levels, induction of mitochondrial depolarization and membrane permeabilization, and translocation of AIF to the nucleus. Of note, N-acetyl-L-cysteine and necrostatin-1, but not z-VAD-fmk, completely prevented glutamate-induced cell death, implying that oxidative stress and AIF translocation were pivotal in glutamate cytotoxicity. DMLE significantly recovered glutamate-induced apoptotic cell death in a concentration-dependent manner. It completely inhibited intracellular/mitochondrial ROS generation, the elevation of Ca levels, and mitochondrial dysfunction induced by glutamate during early exposure within 8 h. It significantly reversed subsequent AIF nuclear translocation after 12 h of treatment. Antioxidant activities of DMLE may be the protective mechanism that regulates homeostatic balance of ROS and Ca as well as maintains mitochondrial function.

Conclusions: DMLE shows significant neuroprotective effects against glutamate-induced oxidative neuronal cell death. Therefore, DM could be a potential therapeutic candidate for neurological disorders propagated by glutamate toxicity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jep.2019.112518DOI Listing
April 2020

Plastome evolution and phylogeny of subtribe Aeridinae (Vandeae, Orchidaceae).

Mol Phylogenet Evol 2020 03 21;144:106721. Epub 2019 Dec 21.

Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea. Electronic address:

Subtribe Aeridinae (Vandeae, Epidendroideae, Orchidaceae) consists of 83 genera and 2,345 species. The present study completely decoded the plastomes and nuclear ribosomal (nr) RNA gene clusters of seven species of Aeridinae belonging to Gastrochilus, Neofinetia, Pelatantheria, and Thrixspermum and compared them with existing data to investigate their genome evolution and phylogeny. Although no large structural variations were observed among the Aeridinae plastomes, 14 small inversions (SI) were found in Orchidaceae for the first time. Therefore, the evolutionary trends and usefulness of SI as molecular identification markers were evaluated. Since all 11 ndh genes in the Aeridinae plastome were lost or pseudogenized, the evolutionary trends of ndh genes are discussed at the tribe and family levels. In the maximum likelihood tree reconstructed from 83 plastome genes, the five Orchidaceae subfamilies were shown to have diverged in the following order: Apostasioideae, Vanilloideae, Cypripedioideae, Orchioideae, Epidendroideaeae. Divergence times for major lineages were found to be more recent, 5-10 Mya, than previous studies, which only used two or three genes. Vandeae, which includes Aeridinae, formed a sister group with Cymbidieae and Epidendreae. The Vandeae, Cymbidieae, and Epidendreae lineages were inferred to have diverged at 25.31 Mya; thus, numerous speciation events within Aeridineae occurred since then. Furthermore, the present study reconstructed a phylogenetic tree from 422 nrITS sequences belonging to Aerdinae and allied taxa and uses it to discuss the phylogenetic positions and species identities of five endangered species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ympev.2019.106721DOI Listing
March 2020

The complete chloroplast genome of a rare species in Korea, Ker Gawl.

Mitochondrial DNA B Resour 2019 Oct 15;4(2):3591-3592. Epub 2019 Oct 15.

Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea.

Ker Gawler is a wild lily species that belongs to section Sinomartagon and is one of the ancestors of the Asiatic hybrid lilies. Unique traits such as disease resistance and early flowering make a desirable resource for interspecific hybridization. However, in Korea, the natural resources of are being exhausted by excessive exploitation and require urgent conservation. In this study, the complete chloroplast genome of was generated using Illumina paired-end sequencing technology, and its structure was compared with that of other species. The chloroplast genome was 152,063 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (26,492 bp) separated by a large (81,485 bp) and small (17,584 bp) single-copy (SC) region. The genome encodes 131 different genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A phylogenetic analysis strongly supported the relationship of with other members of Sinomartagon and Martagon lilies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2019.1676174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7707306PMC
October 2019

Characterization of the complete chloroplast genome sequence of the giant knotweed, from the volcanic island Dokdo, Republic of Korea.

Mitochondrial DNA B Resour 2019 Sep 12;4(2):2972-2973. Epub 2019 Sep 12.

Department of Life Sciences, Yeungnam University, Gyeongsan, Republic of Korea.

The giant knotweed plant, is confined to Ulleung and Dokdo islands, Korea. Here, we reported the complete chloroplast genome of . The chloroplast genome size was 163,485 bp in length, containing a couple of identical inverted repeat regions of 31,108 bp, a large single-copy region of 87,703 bp and small single-copy region of 13,566 bp. The genome encoded 129 genes, of which 112 were unique, including 78 protein-coding, 30 tRNA and 4 rRNA genes. The maximum-likelihood phylogenetic tree showed that F. sachalinensis is a basal group and sister to the rest of the Polygonaceae family plants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2019.1663769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7706866PMC
September 2019

The complete chloroplast genome sequence of (Caryophyllaceae).

Mitochondrial DNA B Resour 2019 Jul 16;4(2):2570-2571. Epub 2019 Jul 16.

National Institute of Biological Resources, Incheon, Republic of Korea.

The complete chloroplast genome sequence of Makino (Caryophyllaceae) was determined. The genome was 151,831 bp long, consisting of a large single-copy region (83,875 bp) and a small single-copy region (17,591 bp) separated by two inverted repeats (25,331 bp). The plastome contained 124 genes; 82 encode proteins, 34 encode tRNA, and eight encode rRNA. The gene quantity and order resembled those of a typical Caryophyllaceae plastome. Phylogenetic analysis using 79 gene sequences from 14 previously reported genomes of Caryophyllaceae showed that clades were nested within the genus, suggesting that is a lower taxonomic rank than genus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2019.1639556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7687520PMC
July 2019

Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb "Bang-Poong".

Int J Mol Sci 2019 May 4;20(9). Epub 2019 May 4.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

Three Apiaceae species , , and are used as Asian herbal medicines, with the confusingly similar common name "Bang-poong". We characterized the complete chloroplast (cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences of two accessions for each species. The complete cp genomes of , , and were 147,467, 147,830, and 164,633 bp, respectively. Compared to the other species, the cp genome had a huge inverted repeat expansion and a segmental inversion. The 45S nrDNA cistron sequences of the three species were almost identical in size and structure. Despite the structural variation in the cp genome, phylogenetic analysis revealed that diverged 5-6 million years ago (Mya), while diverged from only 2-3 Mya. Abundant copy number variations including tandem repeats, insertion/deletions, and single nucleotide polymorphisms, were found at the interspecies level. Intraspecies-level polymorphism was also found for and . We developed nine PCR barcode markers to authenticate all three species. This study characterizes the genomic differences between , , and ; provides a method of species identification; and sheds light on the evolutionary history of these three species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms20092196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6539805PMC
May 2019

The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species.

PLoS One 2019 20;14(3):e0214162. Epub 2019 Mar 20.

Department of Biological Sciences, Kangwon National University, Chuncheon, Gangwon, South Korea.

We report the complete chloroplast genomes of four Viola species (V. mirabilis, V. phalacrocarpa, V. raddeana, and V. websteri) and the results of a comparative analysis between these species and the published plastid genome of the congeneric species V. seoulensis. The total genome length of the five Viola species, including the four species analyzed in this study and the species analyzed in the previous study, ranged from 156,507 (V. seoulensis) to 158,162 bp (V. mirabilis). The overall GC contents of the genomes were almost identical (36.2-36.3%). The five Viola plastomes each contained 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Among the annotated genes, 16 contained one or two introns. Based on the results of a chloroplast genome structure comparison using MAUVE, all five Viola plastomes were almost identical. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved among the Viola species. A total of 259 exon, intron, and intergenic spacer (IGS) fragments were compared to verify the divergence hotspot regions. The nucleotide diversity (Pi) values ranged from 0 to 0.7544. The IR region was relatively more conserved than the LSC and SSC regions. The Pi values in ten noncoding regions were relatively high (>0.03). Among these regions, all but rps19-trnH, petG-trnW, rpl16-rps3, and rpl2-rpl23 represent useful molecular markers for phylogenetic studies and will be helpful to resolve the phylogenetic relationships of Viola. The phylogenetic tree, which used 76 protein-coding genes from 21 Malpighiales species and one outgroup species (Averrhoa carambola), revealed that Malpighiales is divided into five clades at the family level: Erythroxylaceae, Chrysobalanaceae, Euphorbiaceae, Salicaceae, and Violaceae. Additionally, Violaceae was monophyletic, with a bootstrap value of 100% and was divided into two subclades.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214162PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426196PMC
December 2019

Genetic diversity and population structure of Lychnis wilfordii (Caryophyllaceae) with newly developed 17 microsatellite markers.

Genes Genomics 2019 04 30;41(4):381-387. Epub 2018 Nov 30.

Plant Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.

Lychnis wilfordii (Regel) Maxim. is a perennial plant designated as an endangered species by the Korean government because of rapid reduction in its population size. Thus, a population genetic study of this species is needed to establish the strategy for management and conservation based on scientific evidences. The goals of this study were to develop useful microsatellite markers for L. wilfordii and to understand current genetic status of L. wilfordii in Korean peninsula. Seventeen microsatellite markers were identified using next-generation sequencing and bioinformatic analysis and then analyzed genetic diversity in one hundred forty-five individuals from Korea (KI1, KI2, and KP), China (CX, CF) and Russia (RP). Analysis of molecular variance (AMOVA), principal coordinates analysis (PCoA) and STRUCTURE results consistently showed discontinuity among L. wilfordii populations. AMOVA showed that the percentage of variation among populations was 53%, which was higher than the variation within populations (19%). PCoA showed that the populations were divided into three genetic clusters, (1) Chinese (CX, CF), (2) Russian (RP) populations and Korean populations (KI1, KI2) excluding KP, and (3) the KP population. In particular, KP, the most southern population on the Korean peninsula, showed significantly lower observed and expected heterozygosity, number of effective alleles, and Shannon index (I) than those of KI1 and KI2. L. wilfordii showed high differentiation between populations with low genetic diversity within populations. Among Korean populations, KP is likely to be affected by genetic drift due to small population size, low genetic diversity and limited gene flow.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13258-018-0759-0DOI Listing
April 2019

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

PLoS One 2018 22;13(6):e0199626. Epub 2018 Jun 22.

Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199626PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6014681PMC
December 2018

Characterization of the complete chloroplast genome of Arabis stellari and comparisons with related species.

PLoS One 2017 15;12(8):e0183197. Epub 2017 Aug 15.

Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea.

Arabis stellari var. japonica is an ornamental plant of the Brassicaceae family, and is widely distributed in South Korea. However, no information is available about its molecular biology and no genomic study has been performed on A. stellari. In this paper, the authors report the complete chloroplast genome sequence of A. stellari. The plastome of A. stellari was 153,683 bp in length with 36.4% GC and included a pair of inverted repeats (IRs) of 26,423 bp that separated a large single-copy (LSC) region of 82,807 bp and a small single-copy (SSC) region of 18,030 bp. It was also found to contain 113 unique genes, of which 79 were protein-coding genes, 30 were transfer RNAs, and four were ribosomal RNAs. The gene content and organization of the A. stellari chloroplast genome were similar to those of other Brassicaceae genomes except for the absence of the rps16 protein-coding gene. A total of 991 SSRs were identified in the genome. The chloroplast genome of A. stellari was compared with closely related species of the Brassicaceae family. Comparative analysis showed a minor divergence occurred in the protein-coding matK, ycf1, ccsA, accD and rpl22 genes and that the KA/KS nucleotide substitution ratio of the ndhA genes of A. stellari and A. hirsuta was 1.35135. The genes infA and rps16 were absent in the Arabis genus and phylogenetic evolutionary studies revealed that these genes evolved independently. However, phylogenetic analysis showed that the positions of Brassicaceae species are highly conserved. The present study provides A. stellari genomic information that may be found useful in conservation and molecular phylogenetic studies on Brassicaceae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183197PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557495PMC
October 2017

Development of microsatellite markers based on expressed sequence tags in (Asparagaceae).

Appl Plant Sci 2017 Apr 18;5(4). Epub 2017 Apr 18.

Department of Life Science, Hallym University, Chuncheon 24252, Republic of Korea.

Premise Of The Study: Transcriptome-derived simple sequence repeat (SSR) markers were developed in (Asparagaceae). Due to its application in traditional medicine, its wild populations are threatened by over-collection even in protected areas, requiring immediate conservation efforts.

Methods And Results: Based on transcriptome data of , 96 primer pairs with two to seven alleles per locus were selected for initial validation; of those, 27 primer pairs amplified across all samples, resulting in 15 polymorphic and 12 monomorphic microsatellite markers. The usefulness of these markers was assessed in 60 individuals representing three populations of . Observed and expected heterozygosity values ranged from 0.050 to 0.950 and 0.049 to 0.626, respectively. Cross-species amplification of the 27 markers was tested in the related species . and .

Conclusions: These polymorphic, transcriptome-derived SSR markers can be used as molecular markers to study population genetics and ecological conservation in and related taxa.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3732/apps.1700021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400436PMC
April 2017

The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

PLoS One 2017 27;12(2):e0172924. Epub 2017 Feb 27.

Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea.

The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172924PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5328339PMC
September 2017

Isolation and characterization of microsatellite markers in the complex (Polypodiaceae).

Appl Plant Sci 2016 Oct 12;4(10). Epub 2016 Oct 12.

State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.

Premise Of The Study: Microsatellites were designed and characterized in the Sino-Himalayan fern complex (Polypodiaceae) to further study the phylogeography and reproductive ecology of this species.

Methods And Results: From a genomic library obtained by next-generation sequencing, 10 polymorphic and six monomorphic microsatellite loci were developed. In one population of from Taibaishan in central China, the number of alleles observed for these microsatellites ranged from seven to 29, and observed and expected heterozygosity ranged from 0.463 to 0.919 and from 0.797 to 0.947, respectively. Cross-amplification in other taxa within this complex was successful, but cross-amplification was poor for other congeneric species.

Conclusions: This set of newly developed microsatellite markers will be useful for assessing genetic diversity, population structure, and mating system, and to infer polyploid origin in the complex.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3732/apps.1600069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5077284PMC
October 2016

DNA Barcoding of Metazoan Zooplankton Copepods from South Korea.

PLoS One 2016 6;11(7):e0157307. Epub 2016 Jul 6.

School of Life Sciences, Graduate School, Kyungpook National University, Daegu, South Korea.

Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis-Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae-Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica-Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica-Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157307PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934703PMC
August 2017

The complete mitochondrial genome of Brachymystax lenok tsinlingensis (Salmoninae, Salmonidae) and its intraspecific variation.

Gene 2015 Dec 16;573(2):246-53. Epub 2015 Jul 16.

National Institute of Biological Resources, Environmental Research Complex, Incheon 404-708, Republic of Korea. Electronic address:

The Manchurian trout, Brachymystax lenok tsinlingensis, is endangered in Korea, where the southern range limit for this cold-freshwater fish occurs. In this study, the complete mitochondrial genome of Korean B. lenok tsinlingensis was sequenced and its genetic characteristics were identified. The mitogenome of B. lenok tsinlingensis comprises 16,748 base pairs containing 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) and one major non-coding region (control region), making it similar to the majority of vertebrate mitogenomes. Interestingly, at the base of the stem region of OL in B. lenok tsinlingensis, the conserved motif is replaced by a 5'-ACCGG-3' motif instead of the 5'-GCCGG-3'. We also identified an 81-base-pair tandem-repeat motif in the control region, the length of which is reduced by one nucleotide compared to those in B. lenok and Hucho species. The number of repeat motifs differed between Korean and Chinese B. lenok tsinlingensis, with two and three reiterations, respectively. The control region of B. lenok and its relatives will be used as a genetic marker in evolution/genetic studies and as a PCR-based marker for rapid identification of their lineages.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gene.2015.07.049DOI Listing
December 2015

Diagnosis of an unidentified sturgeon species using the complete mitochondrial DNA.

Mitochondrial DNA 2015 10;26(5):811-2. Epub 2014 Jan 10.

b Marine Biology Center for Research and Education, Gangneung-Wonju National University , Gangneung , Korea.

A sturgeon of unknown species of 11 kg body weight was caught in Gosung-gun, Gangwon Province, Korea (38°17'10.67″N, 128°33'20.28″E). The morphological characteristics were similar to species of the genus Acipenser such as Acipenser medirostris, A. schrenckii and A. baerii, but it was not an obvious match. To identify the species using genetic tools, we analysed the complete mitogenome of this unidentified sturgeon, and found it to comprise 16,526 bp. The genome encoded 2 rRNAs, 22 tRNAs, 13 protein-coding genes and 1 control region. The nucleotide divergence between the complete mitogenome of the unidentified sturgeon and those of four Acipenser spp. (A. transmontanus, A. dabryanus, A. schrenckii and A. baerii) was 0.736%, 3.875%, 0.085% and 5.580%, respectively. This study suggests that the unidentified sturgeon is able to predict the least maternal lines with A. schrenckii.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3109/19401736.2013.855905DOI Listing
June 2016

Development of microsatellite markers in Pungtungia herzi using next-generation sequencing and cross-species amplification in the genus Pseudopungtungia.

Int J Mol Sci 2013 Oct 1;14(10):19923-31. Epub 2013 Oct 1.

National Institute of Biological Resources, Incheon 404-708, Korea.

Nuclear microsatellite markers for Pungtungia herzi were developed using a combination of next-generation sequencing and Sanger sequencing. One hundred primer sets in the flanking region of dinucleotide and trinucleotide repeat motifs were designed and tested for efficiency in polymerase chain reaction amplification. Of these primer sets, 16 new markers (16%) were successfully amplified with unambiguous polymorphic alleles in 16 individuals of Pungtungia herzi. Cross-species amplification with these markers was then examined in two related species, Pseudopungtungia nigra and Pseudopungtungia tenuicorpa. Fifteen and 11 primer pairs resulted in successful amplification in Pseudopungtungia nigra and Pseudopungtungia tenuicorpa, respectively, with various polymorphisms, ranging from one allele (monomorphic) to 11 alleles per marker. These results indicated that developing microsatellite markers for cross-amplification from a species that is abundant and phylogenetically close to the species of interest is a good alternative when tissue samples of an endangered species are insufficient to develop microsatellites.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms141019923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821594PMC
October 2013

The complete mitochondrial genome sequence of the Korean hare (Lepus coreanus).

Mitochondrial DNA 2015 Feb 25;26(1):129-30. Epub 2013 Jul 25.

National Institute of Biological Resources , Incheon , Korea and.

The complete mitogenome of the Korean hare (Lepus coreanus) was determined by the long and accurate polymerase chain reaction and primer-walking methods. The mitogenome of the Korean hare is 17,472 bp in length and contains sequences that encode 13 protein genes, 22 tRNAs, 2 rRNAs and a noncoding control region. The mitogenome is arranged in an identical order to that found in most other vertebrates. All mitochondrial genes are encoded on the heavy strand, except for eight tRNA genes and the ND6 gene. The control region contains putative termination associated elements, conserved sequence blocks and short and long tandem repeats motifs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3109/19401736.2013.815170DOI Listing
February 2015

Complete mitochondrial genome sequence of a Korean Pungtungia herzi (Cypriniformes, Gobioninae).

Mitochondrial DNA 2014 Dec 10;25(6):414-5. Epub 2013 Jul 10.

National Institute of Biological Resources, Environmental Research Complex , Incheon , South Korea.

The mtDNA sequence of Pungtungia herzi in Korea comprises 16,599 nt and contains 37 genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs). The content and the arrangement of the genome of the Korean specimen were identical to that previously reported for a Japanese specimen, with 98.3% genetic similarity between the two complete mitogenomes. The pairwise distances of three complete mitogenomes obtained among Pungtungia herzi and Pseudopongtungia nigra. Pungtungia herzi and Pseudopongtungia tenuicorpa, and Pungtungia nigra and Pseudopongtungia tenuicorpa were 9.26%, 12.88% and 12.75%, respectively.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3109/19401736.2013.809435DOI Listing
December 2014

DNA barcode reference data for the Korean herpetofauna and their applications.

Mol Ecol Resour 2013 Nov 11;13(6):1019-32. Epub 2013 Jan 11.

National Institute of Biological Resources, Environmental Research Complex, Incheon, 404-708, South Korea.

Recently, amphibians and reptiles have drawn attention because of declines in species and populations caused mainly by habitat loss, overexploitation and climate change. This study constructed a DNA barcode database for the Korean herpetofauna, including all the recorded amphibians and 68% of the recorded reptiles, to provide a useful, standardized tool for species identification in monitoring and management. A total of 103 individuals from 18 amphibian and 17 reptile species were used to generate barcode sequences using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and to compare it with other suggested barcode loci. Comparing 16S rRNA, cytochrome b (Cytb) and COI for amphibians and 12S rRNA, Cytb and COI for reptiles, our results revealed that COI is better than the other markers in terms of a high level of sequence variation without length variation and moderate amplification success. Although the COI marker had no clear barcoding gap because of the high level of intraspecific variation, all of the analysed individuals from the same species clustered together in a neighbour-joining tree. High intraspecific variation suggests the possibility of cryptic species. Finally, using this database, confiscated snakes were identified as Elaphe schrenckii, designated as endangered in Korea and a food contaminant was identified as the lizard Takydromus amurensis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1755-0998.12055DOI Listing
November 2013

Insights into Korean red fox (Vulpes vulpes) based on mitochondrial cytochrome b sequence variation in East Asia.

Zoolog Sci 2012 Nov;29(11):753-60

National Institute of Biological Resources, Environmental Research Complex, lncheon, Korea.

The red fox (Vulpes vulpes) is the most widely distributed terrestrial carnivore in the world, occurring throughout most of North America, Europe, Asia, and North Africa. In South Korea, however, this species has been drastically reduced due to habitat loss and poaching. Consequently, it is classified as an endangered species in Korea. As a first step of a planned red fox restoration project, preserved red fox museum specimens were used to determine the genetic status of red foxes that had previously inhabited South Korea against red foxes from neighboring countries. Total eighty three mtDNA cytochrome b sequences, including 22 newly obtained East Asian red fox sequences and worldwide red fox sequences from NCBI, were clustered into three clades (i.e., I, II, and III) based on haplotype network and neighbor-joining trees. The mean genetic distance between clades was 2.0%. Clade III contained South Korean and other East Asian samples in addition to Eurasian and North Pacific individuals. In clade III, South Korean individuals were separated into two lineages of Eurasian and North Pacific groups, showing unclear phylogeographic structuring and admixture. This suggests that South Korean red fox populations may have been composed of individuals from these two different genetic lineages.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2108/zsj.29.753DOI Listing
November 2012