Chong-Wook Park

A DNA barcode for land plants

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

Phylogenetic relationships in family Magnoliaceae inferred from ndhF sequences

The ndhF sequences of 99 taxa, representing all sections in extant Magnoliaceae, were analyzed to address phylogenetic questions in the family. Magnolia macrophylla and M. dealbata, North American species of Magnolia section Rytidospermum, are placed at the base in the subfamily Magnolioideae although its supporting value is low. In the remaining taxa, several distinctive lineages are recognized: (1) Magnolia, the biggest genus in the family, is not monophyletic; (2) Michelia, including section Maingola of Magnolia subgenus Magnolia, is closely related with Elmerrillia and sections Alcimandra and Aromadendron of Magnolia subgenus Magnolia; (3) the associates of Michelia are grouped with Magnolia subgenus Yulania and section Gynopodium of Magnolia subgenus Magnolia; (4) Pachylarnax forms a clade with sections Manglietiastrum and Gynopodium of Magnolia; (5) a well-supported Manglietia clade is recognized; (6) Caribbean species of section Theorhodon of Magnolia subgenus Magnolia, which are section Splendentes sensu Vázquez-Garcia, are closely allied with New World members of Magnolia subgenus Talauma; and (7) section Rytidospermum of Magnolia subgenus Magnolia and subgenus Talauma are polyphyletic. The separated clades in the molecular tree are considerably different from traditional taxonomic dispositions in the family. The molecular data strongly suggest that a taxonomic realignment of infrafamilial delimitations and compositions should be considered.

Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia , and its evolutionary implications

The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast matK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our molecular trees support Ohwi’s original treatment of Megaleranthis saniculiforia to Trollius chosenensis Ohwi.

Landscape-level spatial genetic structure in Quercus acutissima (Fagaceae)

Quercus acutissima (Fagaceae), a deciduous broad-leaved tree, is an important forest element in hillsides of South Korea. We used allozyme loci, Wrights F statistics, and multilocus spatial autocorrelation statistics to examine the distribution of genetic diversity within and among three local populations and the spatial genetic structure at a landscape scale (15 ha, 250 × 600 m) on Oenaro Island, South Korea. Levels of genetic diversity in Q. acutissima populations were comparable to mean values for other oak species. A moderate but significant deficit of heterozygotes (mean F(IS) = 0.069) was detected within local populations and low but significant differentiation was observed among populations (F(ST) = 0.010). Spatial autocorrelation analyses revealed little evidence of significant genetic structure at spatial scales of 100-120 m. The failure to detect genetic structure within populations may be due to intraspecific competition or random mortality among saplings, resulting in extensive thinning within maternal half-sib groups. Alternatively, low genetic differentiation at the landscape scale indicates substantial gene flow among local populations. Although wind-borne pollen may be the primary source of gene flow in Q. acutissima, these results suggest that acorn movement by animals may be more extensive than previously anticipated. Comparison of these genetic data for Oenaro Island with a disturbed isolated inland population suggests that population-to-population differences in internal genetic structure may be influenced by local variation in regeneration environment (e.g., disturbance).

Morphological and chromosomal variation in Fallopia section Reynoutria (Polygonaceae) in Korea.

We have examined morphological and chromosomal variation inFallopia sect.Reynoutria in Korea to clarify their taxonomic identities and to determine whether their morphological variability is associated with ploidy levels. Principal components analysis (PCA) of individuals from 21 populations, using major distinguishing characters, revealed the presence of four major entiries of sect.Reynoutria in Korea; these includeF. sachalinensis, F. japonica var.japonica, F. forbesii, and the Nonsan population consisting of presumed hybrids. Based on morphology, it is hypothesized that the Nonsan population was probably derived from multiple hybridization events involving the three named taxa. The results also indicate thatF. forbesii is distinct fromF. japonica var.japonica. Polyploidy is more prevalent in sect.Reynoutria than has been previously recognized.Fallopia sachalinensis in Korea occurs as dodecaploids with 2n=132; our count is the first dodecaploid count for the species, and represents the highest chromosome number known in the genus.Fallopia japonica var.japonica occurs as tetraploids (2n=44), hexaploids (2n=66), and octoploids (2n=88), whileF. forbesii occurs as hexaploids (2n=66) and octoploids (2n=88); our counts appear to be the first reported chromosome numbers forF. forbesii. Morphological analysis indicates that there is no apparent correlation between the ploidy levels in these taxa and the morphological characters that we have considered in this study except that the tetraploids ofF. japonica var.japonica tend to have somewhat thicker leaves.

Phylogenetic Relationships of Maples (Acer L.; Aceraceae) Implied by Nuclear Ribosomal ITS Sequences

Acer. ITS 1 sequences in twenty-eight species of Acer and a species of Dipteronia in the family Aceraceae ranged from 220 to 242 bp and ITS 2 sequences from 215 to 251 bp. The size of the 5.8S coding region was 164 bp for all species examined in the family. Phylogenetic analysis of ITS sequences placed a very robust clade of section Palmata at the base of the tree. Three species of section Parviflora sensu de Jong (1994), A. spicatum, A. distylum and A. nipponicum, did not form a monophyletic clade. Acer spicatum was separated from the robust clade of A. distylum and A. nipponicum. Molecular tree strongly supports the close relationship among section Platanoidea, Glabra series Arguta, and section Macrantha. The close relationship between sections Pentaphylla and Trifoliata was also strongly suggested in ITS tree. Sections Rubra and Hyptiocarpa appeared to be closely allied with each other. The average rate of nucleotide substitution was estimated as (8.0±1.9)×10−11 substitutions per site per year for ITS 1 and (9.0±1.6) ×10−11 for ITS 2.

Flavonoid chemistry of Polygonum sect. Echinocaulon: a systematic survey

Thirteen species of Polygonum sect. Echinocaulon were examined for leaf flavonoid constituents. Thirty-six flavonoid compounds were isolated and identified, most of which were glycosylated and/or methoxylated derivatives of the flavonols kaempferol, quercetin, and myric- etin, and of the flavones apigenin and luteolin. Among them, quercetin 3-0-glycosides were major flavonoid constituents, and present in all species. Species of section Echinocaulon exhibit relatively complex patterns of leaf flavonoid constituents. Although the flavonoid data for some species are lacking, those available appear to be very useful for species delimitation and for recognizing species relationships in the section. Most species of section Echinocaulon are readily distinguished by their flavonoid profiles, and the cladogram based on nine flavonoid characters suggests four basic chem- ical lineages in the section. Section Echinocaulon of Polygonum (Polygo- naceae), first recognized by Meisner (1832), is morphologically distinct and characterized by recurved prickles on the angles of the stems, petioles, and midribs. Additional characters separating this from other sections of Polygo- num include scandent to climbing habit and el- liptic to triangular leaf shapes with sagittate to

DNA barcoding of Orchidaceae in Korea

Species of Orchidaceae are under severe threat of extinction mainly due to overcollection and habitat destruction; accurate identification of orchid species is critical in conservation biology and sustainable utilization of orchids as plant resources. We examined 647 sequences of the cpDNA regions rbcL, matK, atpF‐atpH IGS, psbK‐psbI IGS and trnH‐psbA IGS from 89 orchid species (95 taxa) and four outgroup taxa to develop an efficient DNA barcode for Orchidaceae in Korea. The five cpDNA barcode regions were successfully amplified and sequenced for all chlorophyllous taxa, but the amplification and sequencing of the same regions in achlorophyllous taxa produced variable results. psbK‐psbI IGS showed the highest mean interspecific K2P distance (0.1192), followed by matK (0.0803), atpF‐atpH IGS (0.0648), trnH‐psbA IGS (0.0460) and rbcL (0.0248). The degree of species resolution for individual barcode regions ranged from 60.5% (rbcL) to 83.5% (trnH‐psbA IGS). The degree of species resolution was significantly enhanced in multiregion combinations of the five barcode regions. Of the 26 possible combinations of the five regions, six provided the highest degree of species resolution (98.8%). Among these, a combination of atpF‐atpH IGS, psbK‐psbI IGS and trnH‐psbA IGS, which comprises the least number of DNA regions, is the best option for barcoding of the Korean orchid species.

Flavonoid chemistry of Fallopia section Fallopia (Polygonaceae).

Five controversial species of Fallopia sect. Fallopia sensu Holub were examined for leaf flavonoid constituents. Twenty-one flavonoid compounds were isolated and identified; they were glycosylated derivatives of the flavonols kaempferol, quercetin, and myricetin, and of the flavones apigenin and luteolin. Among them, quercetin 3-O-galactoside and quercetin 3-O-glucoside were major flavonoid constituents and present in all species. Although the flavonoid data for some species are lacking, those available appear to be useful for species delimitation and for recognizing species relationships in the section. The flavonoid data, in conjunction with morphological evidence, strongly suggest that F. scandens, F. dentatoalata, F. dumetorum, and F. convolvulus are closely allied but distinct species. In addition, the flavonoid data for F. cilinodis lend additional support to the segregation of sect. Parogonum from sect. Fallopia.

Flavonoid variation of theAconitum jaluense complex (Ranunculaceae) in Korea

Thirteen flavonoid compounds were isolated and identified from five Korean species in theA. jaluense complex; they were glycosylated derivatives of the flavonols kaempferol, quercetin, and isorhamnetin, and of the flavone apigenin. The flavonoid data revealed the presence of two entities in the complex in Korea; one includesA. jaluense s. str. and the other includes the remaining four species which have identical flavonoid profiles. Based on these results, in conjunction with evidence from the morphology, it is suggested that the taxa should be recognized as two sub-species ofA. jaluense s. l. The flavonoid data also provide strong evidence for the occurrence of hybridization betweenA. jaluense s. str. andA. japonicum subsp.napiforme at Mt. Chiri in southern Korea.