• ALGAE
• /
• v.35 no.3
• /
• pp.293-301
• /
• 2020

The applications of DNA barcoding have a wide range of uses, such as in taxonomic studies to help elucidate cryptic species and phylogenetic relationships and analyzing environmental samples for biodiversity monitoring and conservation assessments of species. After obtaining the DNA barcode sequences, sequence similarity-based homology analysis is commonly used. This means that the obtained barcode sequences are compared to the DNA barcode reference databases. This bioinformatic analysis necessarily implies that the overall quantity and quality of the reference databases must be stringently monitored to not have an adverse impact on the accuracy of species identification. With the development of next-generation sequencing techniques, a noticeably large number of DNA barcode sequences have been produced and are stored in online databases, but their degree of validity, accuracy, and reliability have not been extensively investigated. In this study, we investigated the extent to which the amount and types of erroneous barcode sequences were deposited in publicly accessible databases. Over 4.1 million sequences were investigated in three largescale DNA barcode databases (NCBI GenBank, Barcode of Life Data System [BOLD], and Protist Ribosomal Reference database [PR2]) for four major DNA barcodes (cytochrome c oxidase subunit 1 [COI], internal transcribed spacer [ITS], ribulose bisphosphate carboxylase large chain [rbcL], and 18S ribosomal RNA [18S rRNA]); approximately 2% of erroneous barcode sequences were found and their taxonomic distributions were uneven. Consequently, our present findings provide compelling evidence of data quality problems along with insufficient and unreliable annotation of taxonomic data in DNA barcode databases. Therefore, we suggest that if ambiguous taxa are presented during barcoding analysis, further validation with other DNA barcode loci or morphological characters should be mandated.

• ALGAE
• /
• v.35 no.4
• /
• pp.303-324
• /
• 2020

Cocconeis coreana and C. sijunghoensis are described as new based on micromorphological and molecular data. C. coreana is represented by five unialgal cultures from four different freshwater bodies, two from North Korea and three from South Korea. C. sijunghoensis is represented by two unialgal cultures from a brackish water body in North Korea. Except for one, all of the strains auxosporulated and showed an almost quadrupling of size in length and width. Morphologically, these species with their two different elliptical valves belong to the Cocconeis placentula group. The raphe valve has striae with uniseriate areolae continuing across a pronounced submarginal hyaline rim to the edge of the valve. The sternum valve has uniseriate dash-like areolae continuously from the valve face until the valve edge. Micromorphologically, these species possess two different open valvocopulae: only the raphe valvocopula has fimbriae; the sternum valvocopula has none. Based on p-distances of currently available DNA sequence data, i.e., rbcL and 18SV4, both species are pronouncedly different from the epitype strain of C. placentula, with C. coreana closest to the published molecular data of the strain UTEX FD23 named C. placentula from Iowa, USA, while C. sijunghoensis is closest but not the same as the published molecular data of strain D36_012, the epitype strain of C. placentula from Berlin, Germany. Based on scanning electron microscope observations, differentiating features are discussed concerning valvocopula fimbriae, central area, areolation of the sternum valve and on the raphe valve especially between the submarginal hyaline rim and edge.

• ALGAE
• /
• v.31 no.4
• /
• pp.303-315
• /
• 2016

Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecular markers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified and used to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological types from China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences between the Chinese samples implied that they were introduced by different dispersal events and from varied origins. It was speculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodinia supercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era.Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in the current monospecific global distribution. Additional global specimens and sequence information were required to increase our understanding of the evolutionary history of this ancient red algal lineage.

• Journal of fish pathology
• /
• v.26 no.3
• /
• pp.295-301
• /
• 2013

Ferritin is an evolutionarily conserved protein that plays an important role in iron storage and detoxification. In this study, the gene encoding a ferritin H subunit homologue (RbFH) was cloned from rock bream (Oplegnathus fasciatus) and analyzed at the expression. The full-length ferritin H cDNA was 1162 bp long and contained an open reading frame (ORF) of 531 bp that encoded 177 amino acid residues with a predicted molecular mass of 20.8 kDa. The 5' UTR was 297 bp in length, and the 3' UTR 298 bp, and preceded by a 5'-untranslated region that contains a putative Iron Regulatory Element (IRE). The deduced amino acid sequence of RbFH shares extensive sequence identities with the H ferritins of a number of fish species and contains the ferroxidase center that is preserved in ferritin H subunits. Examination of tissue specific expression indicated that RbFH expression was most abundant in PBLs, RBC, liver and muscle.

• ALGAE
• /
• v.25 no.2
• /
• pp.71-76
• /
• 2010

Centroceras gasparrinii is characterized by 1) straight spines, 2) an ovoid gland cell, 3) tetrasporangia with involucral branchlets, and 4) ovoid cortical cells on the first and second cortical initials. A similar Centroceras species with dichotomous habit, "Centroceras clavulatum", has been widely known as a common species of Korean marine flora. However, the species known as "C. clavulatum" in Korea is recognized as C. gasparrinii based on the molecular and morphological evidence. Newly generated sequences of rbcL gene reveal that all taxa of Centroceras from Korea having dichotomous branching pattern are C. gasparrinii. There is 0-0.07% sequence divergence among specimens of C. gasparrinii in Korea. "Centroceras clavulatum" is excluded from Korean flora and C. gasparrinii is included instead of "Centroceras clavulatum". C. gasparrinii also differs from C. distichum in Korea in that it has tetrasporangia with involucral branchlets and dichotomous branching pattern, while C. distichum has immersed tetrasporangia and an alternate branching pattern.

• Korean Journal of Plant Taxonomy
• /
• v.43 no.1
• /
• pp.46-55
• /
• 2013

The purpose of this study is to review the taxonomic position of Taxus cuspidata var. latifolia endemic to Ulleung Island with related taxa T. cuspidata var. cuspidata, T. caespitosa, and T. cuspidata var. nana based on external morphological characters and DNA barcoding study. T. cuspidata var. latifolia was similar to T. cuspidata var. cuspidata in the arbor, straight trunk, and symmetric arrangement of leaf. But the unique differences between T. cuspidata var. latifolia and T. cuspidata var. cuspidata were leaf size and the exposure of seed from aril. Additionally, sequences of four chloroplast DNA regions including matK, rbcL, trnL intron and trnL-trnF spacer regions were analyzed. Korean Taxus species and their related taxon T. cuspidata var. nana were strongly supported as a monophyletic group in neighbor-joining analysis. Taxus cuspidata var. latifolia showed 100% sequence identity to related taxa. Korean endemic T. caespitosa is also distinguishable from related taxa by prostrate stems and spiral arrangement of leaf. The examinations of external morphology and DNA barcoding study suggest that the taxonomic position of T. cuspidata var. latifolia should be maintained as a variety of T. cuspidata.

• Korean Journal of Environmental Biology
• /
• v.36 no.2
• /
• pp.150-155
• /
• 2018

Two siphonous green algae were collected from the eastern coast of Korea. These species share the typical features of Derbesia sporophytes, such as erect and prostrate siphonous filaments and the presence of basal septum in lateral branches. One is characterized by the combined features of a relatively small tufted sporophytic thalli arising from a rhizoidal base, subdichotomously branched filaments with a basal septum and one pyrenoid per subspherical to lenticular chloroplast. The other shows a larger sporophytic thallus, sparsely subdichotomously branched filaments with a basal septum and one pyrenoid per spherical chloroplast. In a phylogenetic tree based on rbcL sequence, the two above-mentioned Korean algae nest in the same clades as Derbesia minima and D. indica, respectively. The genetic distance between the sequences within the clades was 0.5-0.8%, which is considered to be included in the intra-specific range for the genus. These two siphonous Korean algae are identified as D. minima and D. indica, respectively, based on the morphological and molecular analyses. These species are newly recorded in the Korean marine algal flora herein.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2018.04a
• /
• pp.37-37
• /
• 2018

The genus Crepidiastrum (Asteraceae), containing ca. 20 species, is mainly distributed in Asia. Crepidiastrum denticulatum, an edible plant that commonly call "e-go-deulppae-gi" in Korean, distributes in Korea, Japan, and China. The complete chloroplast (cp) genome sequences of C. denticulatum was characterized from MiSeq2000 (Illumina Co.) pair-end sequencing data. The cp genome of C. denticulatum has a total sequence length of 152,689 bp and show a typical quadripartite structure. It consists of the large single copy (LSC: 84,022 bp), small single copy (SSC: 18,519 bp), separated by a pair of inverted repeats (IRs: 25,074 bp) and contains 110 unique genes and 18 genes duplicated in the IR regions. Our comparative analysis identified three cpDNA regions (matK, rbcL, and psbA-trnH) from three Crepidiastrum species, which may be useful for molecular identification of each species, and providing a guideline for its clear confirming about dried medical herb.

• Korean Journal of Environmental Biology
• /
• v.36 no.3
• /
• pp.308-313
• /
• 2018

During a survey of marine algal flora, a red algal species was collected from Giseong, Uljin located on the eastern coast of Korea. This species has the generic features of Cryptonemia belonging to Halymeniaceae, and is characterized by the presence of erect foliose thalli arising from a discoid holdfast, somewhat fan-shaped blade with an evanescent midrib at the base, narrow main axes with blade-like wings of slightly undulate margin, a perennial stalk, and entwined filamentous medulla with refractive stellate cells. In a phylogenetic tree based on rbcL sequence, the Korean alga nests in the same clade with C. lomation from France and C. seminervis from Spain. Genetic divergence among the sequences within the clade was not recognized thus suggesting that both the species are conspecific. The name C. lomation considered to be valid nomenclaturally is accepted for the entity. Based on the morphological and molecular analyses, the Korean alga is identified as C. lomation, originally described from Italy. This confirms the occurrence of C. lomation in Korea. The species appears to be distributed in the temperate region influenced more or less by the North Korea Cold Current.

• Korean Journal of Environmental Biology
• /
• v.39 no.3
• /
• pp.383-389
• /
• 2021

The Erythropeltidales are a common group of small, mostly epiphytic, marine red algae. However, they are little known in Korea. Many of the described species of Erythropeltidales differ subtly in morphology, and often the morphological differences are due to the substrate or environmental changes. Integration of molecular data with standardized culture conditions has been recommended to account for these algae. A Madagascaria species was first collected from the western coast of Korea and was identified as Madagascaria erythrocladioides based on the morphological and molecular characteristics. Morphological characteristics conformed well with its original description, and the phylogenetic analysis based on rbcL sequence showed Korean M. erythrocladioides nests in the same clade with the original species described in Japan with a genetic distance of 0.0-0.1%. This species was isolated from a red alga, Pterocladiella capillacea, in laboratory culture. The thallus ontogeny and host preference were examined by a co-culture with 13 different species of algae. Results showed a relatively broad host preference in mono-spore attachment and epiphyte development of Madagascaria erythrocladioides. Mono-spores of M. erythrocladioides attached to most of the red algal hosts' surfaces but no crustose thalli developed on some of the algal hosts even after one month of co-culture.