• Journal of Species Research
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• v.11 no.4
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• pp.287-295
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• 2022

Three oxytrichid ciliates, Oxytricha lithofera Foissner, 2016, Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003 and Sterkiella tetracirrata Kumar et al., 2015, were isolated from soils and confirmed as new to South Korea. Oxytricha lithofera was identified based on lithosomes, cortical granules, 21-33 adoral zone membranelles, one left (14-21 cirri) and one right (15-18) marginal rows and 5 transverse cirri. Pleurotricha curdsi was identified based on the possession of 2 macronuclear nodules, 2-3 micronuclei, 46-53 adoral zone membranelles, 3 frontal cirri, 5 frontoventral cirri, 5-7 postoral ventral cirri, 2-3 right marginal rows and 5 transverse cirri. Sterkiella tetracirrata was identified with respect 4 macronuclear nodules, 3-6 micronuclei, 25-40 adoral zone membranelles, 3 frontal cirri, 3 postoral ventral cirri, 2 pretransverse cirri, one left (21-30 cirri) and one right (24-30) marginal row and 4 transverse cirri. On the basis of 18S rDNA sequence analyses, we describe the phylogenetic positions of the three species.

• Journal of Ecology and Environment
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• v.41 no.1
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• pp.9-18
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• 2017

Background: Species in the heterokont genus Synura are colonial and have silica scales whose ultrastructural characteristics are used for classification. We examined the ultrastructure of silica scales and molecular data (nuclear SSU rDNA and LSU rDNA, and plastid rbcL sequences) to better understand the taxonomy and phylogeny within the section Petersenianae of genus Synura. In addition, we report the first finding of newly recorded Synura species from Korea. Results: We identified all species by examination of scale ultrastructure using scanning and transmission electron microscopy (SEM and TEM). Three newly recorded species from Korea, Synura americana, Synura conopea, and Synura truttae were described based on morphological characters, such as cell size, scale shape, scale size, keel shape, number of struts, distance between struts, degree of interconnections between struts, size of base plate pores, keel pores, base plate hole, and posterior rim. The scales of the newly recorded species, which belong to the section Petersenianae, have a well-developed keel and a characteristic number of struts on the base plate. We performed molecular phylogenetic analyses based on sequence data from three genes in 32 strains (including three outgroup species). The results provided strong statistical support that the section Petersenianae was monophyletic, and that all taxa within this section had well-developed keels and a defined number of struts on the base plate. Conclusions: The phylogenetic tree based on sequence data of three genes was congruent with the data on scale ultrastructure. The resulting phylogenetic tree strongly supported the existence of the section Petersenianae. In addition, we propose newly recorded Synura species from Korea based on phylogenetic analyses and morphological characters: S. americana, S. conopea, and S. truttae.

• Journal of Species Research
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• v.1 no.2
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• pp.232-239
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• 2012

Taxonomy of umbelliferous taxa Heracleum moellendorffii complex has been unclear in their species delimitation in the far-eastern Asian regions. In both Korea and China Heracleum moellendorffii was adopted for their description while H. sphondylium was chosen to describe Japanese Heracleum. From Genbank accessions, taxa collected from Kamtchatka and Promorskiy, Russia were defined as H. maximum, endemic taxon to North America. In this study, we reviewed the taxonomy of Heracleum moellendorffii complex in Korea and neighboring countries on the basis of molecular phylogenies derived from sequences of nuclear ribosomal DNA internal transcribed spacer (ITS) regions. From three Korean accessions of Heracleum investigated in this study, two types of ITS sequences were obtained; two accessions were related to Chinese H. moellendorffii var. moellendorffii and North American H. maximum without forming a clade while the other one was identical to accession from H. maximum from Primorskiy, Russia. In the other hand, Japanese H. moellendorffii (=H. sphondylium ssp. sphondylium var. nipponicum in the flora of Japan) was closely related to H. maximum accessions from Korea and Russia, not nested within the clade comprising several subspecies of H. sphondylium. In order to delimit species boundaries among putatively closely related Heracleum species in fareastern Asian countries, more samples and much more rapidly evolved DNA regions must be investigated with interpretation of morphological and anatomical features.

• Korean Journal of Plant Taxonomy
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• v.40 no.4
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• pp.234-239
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• 2010

The taxonomy of umbel genus Sium L., Apiaceae in Korea was reviewed on the basis of molecular phylogenies derived from sequences of nuclear ribosomal DNA internal transcribed spacer (ITS) regions. The ITS sequence-derived phylogeny indicates that S. heterophyllum, endemic to Korea, is identical to S. tenue, which is known as endemic to Ussuri regions. Comparisons of sequence pairs across both spacer regions gave divergence values and revealed the identity between S. tenue and S. heterophyllum on Mt. Moonsoo. On the other hand, the ITS sequences support species delimitation of S. ternifolium, as reported recently as a new species that differs from other Sium species. The ITS sequence divergence values of 1.4 and 1.6% support species delimitation between S. serra and S. ternifolium.

• Korean Journal of Plant Taxonomy
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• v.39 no.4
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• pp.237-246
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• 2009

Inter-specific relationships among six species and two varieties, belonging to Scrophularia (Scrophulariaceae), in Korea were re-examined based on both morphological and molecular data. Scrophularia takesimensis, a Korean endemic species, should be separated from S. grayana as an independent species based upon unique morphological characters such as non-winged stems, thickened leaves and glabrous surfaces of leaves, even though they share a lot of other features. It was found that S. grayana is distributed in Sokcho in Korea and along the coast of the East Sea north to far eastern Russia. Although some morphologies of three taxa, S. cephalantha, S. koraiensis var. velutina and S. kakudensis var. microphylla appeared to differ from each other, their ITS DNA sequence data was similar to that of S. kakudensis, suggesting that they might better be designated with the later species. The taxonomic position of S. koraiensis, only found in Korea, has been ambiguous, but ITS DNA sequence data in this study revealed that this species is distinct from S. kakudensis. Consequently, we conclude that the genus Scrophularia in Korea includes five species.

• ALGAE
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• v.29 no.2
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• pp.57-73
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• 2014

Amphora Ehrenberg ex Kutzing sensu lato is a common and widespread benthic diatom genus with a taxonomy that has been under continual revision, particularly based on molecular analyses. Although Amphora species have been studied using modern microscopy in recent years, there has not been much progress on molecular characterization of the species, especially in Asia. In this study of Amphora, sampling was carried out from September 2009 to August 2010 in Korean coastal waters. The morphological and molecular characteristics of eight Amphora sensu lato were examined: Amphora marina, A. proteus, Halamphora costata, H. coffeaeformis, H. eunotia, H. holsatica, H. terroris, and Halamphora sp. Based on previous accounts, morphology suggested that A. marina and A. proteus belong to the subgenus Amphora Cleve, which have smooth girdle bands and rather coarse and very distinct areolae on the valve. The other species, H. coffeaeformis, H. costata, H. eunotia, H. holsatica, H. terroris, and Halamphora sp. belong to the subgenus Halamphora Cleve, which was recently elevated to generic status by Levkov 2009, have plicate girdle bands, puncta which do not form straight longitudinal lines, valves which have a narrow ventral portion and apices that are generally rostrate-capitate and recurved. In agreement with analysis based on morphological characteristics, phylogenetic analysis based on small subunit rDNA suggested that the eight Amphora sensu lato species were not a monophyletic group as the morphological classification. Also, the results of molecular work and statistical analysis on all these Amphora sensu lato combined with phylogenic analysis on our geographically representative samples give strong evidence that Halamphora Levkov is independent of Amphora Cleve. Furthermore, in this study, Amphora terroris was transferred Halamphora as Halamphora terroris (Ehrenberg) Wang comb. nov. and Amphora marina was recorded for the first time in Korea.

• Korean Journal of Plant Taxonomy
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• v.44 no.3
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• pp.181-187
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• 2014

The taxonomic status of a new forma, Opuntia humifusa (Raf.) Raf. f. jeollaensis E. J. Kim & S. S. Whang, and the taxonomic relationships of three Korean cladodes were studied based on DNA sequences of three genes. The new forma O. humifusa f. jeollaensis (Wanggasi-Chunnyuncho) is simlilar to O. humifusa (Chunnyuncho), but differ in having both flower with the reddish inner center, and strong and many 3 cm long spines. Molecular studies showed that the new forma grouped into Macrocentra series instead of Humifusa series which included Korean O. humifusa. We designated the new taxa firstly studied here as a new forma, because the taxa have been mainly cultivated in farmlands in Jeolla-do area rather than distributed in nature. The taxonomic relationships of three Korean cladodes are discussed in detail.

• ALGAE
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• v.39 no.2
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• pp.75-96
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• 2024

Rhodomonas (Cryptophyceae) and species assigned to this genus have undergone numerous taxonomic revisions. This also applies to R. marina studied here as it was originally assigned as a species of Cryptomonas and later considered a variation of R. baltica, the type species. Despite being described more than 130 years ago, R. marina still lacks a comprehensive characterization. Light and electron microscopy were employed to delineate a strain from western Greenland. The living cells were 18 ㎛ long and 9 ㎛ wide, elliptical in shape with a pointed to rounded posterior and truncated anterior in lateral view. Two sub-equal flagella emerged from a vestibulum, where also a furrow extended. In transmission electron microscopy, the furrow was associated with a tubular gullet and the pyrenoid embedded in a deeply lobed chloroplast. The chloroplast contained DNA in perforations and was surrounded by starch grains. A tubular nucleomorph was enclosed within the pyrenoid matrix. In scanning electron microscopy, the inner periplast consisted of rectangular plates with rounded edges and posteriorly these were replaced by a sheet-like structure. The water-soluble pigment was Crypto-Phycoerythrin type I (Cr-PE 545). A phylogenetic inference based on SSU rDNA confirmed the identity of strain S18 as a species of Rhodomonas as it clustered with congeners but also Rhinomonas, Storeatula, and Pyrenomonas. These genera formed a monophyletic clade separated from a diverse assemblage of other cryptophyte genera. To further explore the phylogeny of R. marina a concatenated phylogenetic analysis based on the SSU rDNA-ITS1-5.8S rDNA-ITS2-LSU rDNA region was performed but included only closely related species. The secondary structure of nuclear internal transcribed spacer 2 was predicted and compared to similar structures in related species. Using morphological and molecular signatures as diagnostic features the description of R. marina was emended.

• Mycobiology
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• v.40 no.1
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• pp.71-75
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• 2012

In the present study, a phylogenetic analysis was undertaken based on the internal transcribed spacer (ITS) rDNA and partial ${\beta}$-tubulin gene sequence of the $Ganoderma$ species. The size of the ITS rDNA regions from different $Ganoderma$ species varied from 625 to 673 bp, and those of the partial ${\beta}$-tubulin gene sequence were 419 bp. Based on the results, a phylogenetic tree was prepared which revealed that Korean $Ganoderma$ $lucidum$ strains belong in a single group along with a $G.$ $lucidum$ strain from Bangladesh.

• Journal of Microbiology and Biotechnology
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• v.18 no.9
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• pp.1496-1499
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• 2008

A Gram-negative, aerobic, rod-shaped, nonspore-forming bacterial strain, designated Gsoil $357^T$ was isolated from soil sample of a ginseng field in Pocheon Province (South Korea). The isolate contained Q-8 as the predominant ubiquinone and iso-$C_{16:0}$, iso-$C_{17:1}$ ${\omega}9c$, and iso-$C_{15:0}$ as the major fatty acids. The G+C content of the genomic DNA was 69.3 mol%. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Gsoil $357^T$ was most closely related to Lysobacter gummosus (97.6%) and Lysobacter antibioticus (97.6%). However, the DNA-DNA relatedness value between strain Gsoil $357^T$ and its phylogenetically closest neighbors was less than 17%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 357T should be classified as representing a novel species in the genus Lysobacter, for which the name Lysobacter ginsengisoli sp. novo is proposed. The type strain is Gsoil $357^T$ (=KCTC $12602^T$=DSM $18420^T$).