• Journal of Microbiology and Biotechnology
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• v.34 no.5
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• pp.1146-1153
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• 2024

The increasing economic losses associated with growth retardation caused by Enterocytozoon hepatopenaei (EHP), a microsporidian parasite infecting penaeid shrimp, require effective monitoring. The internal transcribed spacer (ITS)-1 region, the non-coding region of ribosomal clusters between 18S and 5.8S rRNA genes, is widely used in phylogenetic studies due to its high variability. In this study, the ITS-1 region sequence (~600-bp) of EHP was first identified, and primers for a polymerase chain reaction (PCR) assay targeting that sequence were designed. A newly developed nested-PCR method successfully detected the EHP in various shrimp (Penaeus vannamei and P. monodon) and related samples, including water and feces collected from Indonesia, Thailand, South Korea, India, and Malaysia. The primers did not cross-react with other hosts and pathogens, and this PCR assay is more sensitive than existing PCR detection methods targeting the small subunit ribosomal RNA (SSU rRNA) and spore wall protein (SWP) genes. Phylogenetic analysis based on the ITS-1 sequences indicated that the Indonesian strain was distinct (86.2% nucleotide sequence identity) from other strains collected from Thailand and South Korea, and also showed the internal diversity among Thailand (N = 7, divided into four branches) and South Korean (N = 5, divided into two branches) samples. The results revealed the ability of the ITS-1 region to determine the genetic diversity of EHP from different geographical origins.

• The Korean Journal of Mycology
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• v.27 no.2 s.89
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• pp.124-131
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• 1999

This study was carried out to identify the phylogenetic relationship among Phellinus species by comparing the DNA sequences of the 5.8S ribosomal DNA (rDNA) and the internal transcribed spacers (ITSs), ITS1 and ITS2 regions. Two primers from the 3' end of 18S rDNA and the 5' end of 28S rDNA sequences were chosen to amplify the specific ITS regions of Phellinus spp. Phellinus strains used in the study were divided into four clusters by the phylogenetic tree based on the amplified regions of ITS and 5.8S rDNA sequences. The first cluster consist of Phellinus hartigii IMSNU 32041 and Phellinus robustus IMSNU 32068, and the second cluster consists of Phellinus linteus strains and Phellinus weirianus IMSNU 32021. Phellinus laevigatus KCTC 6229, KCTC 6230 and Phellinus igniarius KCTC 6227, KCTC 6228 belong to the third cluster. Finally, Phellinus chrysoloma KCTC 6225 and Phellinus chrysoloma KCTC 6226 are the fourth cluster. In the second cluster the differentiation between Phellinus linteus strains and Phellinus weirianus species were not possible by the comparison of the ITS sequences. These results revealed that Phellinus linteus and Phellinus weirianus cannot be established the concept of species level only by the ITS sequences. Therefore, both physiological and molecular biological methods as well as the sequences of type strains are necessary to classify the strains of these two species accurately. The comparison of the ITS sequences of four Phellinus species indicated that the sequences of the ITS1 generally are more divergent than those of the ITS2. Although the ITS sequences are varied in some species, the conserved regions in both ITS1 and ITS2 are useful tool to differentiate the species. Phellinus linteus and related species have their specific sequences in the ITS1 compared to the other species.

• The Korean Journal of Mycology
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• v.47 no.4
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• pp.407-416
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• 2019

A common post-harvest disease of sweetpotato tuber is root rot caused by Fusarium solani in Korea as well as the other countries. Storage root rot disease was monitored earlier on sweetpotato (Ipomoea batatas) in storehouses of different locations in Korea. In the present study, an isolate SPL16124 was choosen and collected from Sweetpotato Research Lab., Bioenergy Crop Research Institute, NICS, Muan, Korea, and confirmed the identification as Fusarium solani by conidial and molecular phylogenetic analysis (internal transcribed spacer ITS and translation elongation factor EF 1-α gene sequences). The isolate was cultured on potato dextrose agar, and conidiation was induced. The fungus was screened for Fusarium root rot on tuber of 14 different varieties. Among the tested variety, Yenjami, Singeonmi, Daeyumi, and Sinjami showed resistant to root rot disease. Additionally, the pathogen was tested for pathogenicity on stalks of these varieties. No symptom was observed on the stalk, and it was confirmed that the disease is tissue specific.

• Journal of Species Research
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• v.3 no.2
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• pp.127-166
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• 2014

Moniligastrids are an important yet often ignored earthworm group commonly found in cultivated soils, especially paddy, in the tropical East. Seven new taxa are: Drawida koreana austri, D. koreana nanjiro, D. koreana shindo, D. odaesan, D. jeombongsan, D. companio and D. csuzdii Blakemore spp. or sub-spp. nov. from Korea. Drawida csuzdii is the first new species from North Korea since Lumbricidae Eisenia koreana (Zicsi, 1972). Historical East Asian moniligastrids are reviewed chronologically and Drawida barwelli (Beddard, 1886), D. japonica (Michaelsen, 1892) and D. siemsseni Michaelsen, 1910 are compared on their museum types. These three taxa were thought similar and related to D. nepalensis Michaelsen, 1907 and its possible synonym D. burchardi Michaelsen, 1903 (priority!) and both of these to prior D. uniqua (Bourne, 1887). Indian Drawida calebi Gates, 1945 is compared to new material of D. japonica from Japan, and D. willsi Michaelsen, 1907 to the new sub-species of D. koreana Kobayashi, 1938 from Korea. Where available, mtDNA COI gene barcodes are provided to help objective determinations and a phylogram is provided with outgroup Ocnerodrilidae Eukerria saltensis (Beddard, 1895) itself found in rice paddy/irrigation. The challenge now is comparison of all early taxa in their various homelands in order to assess the genetic variability and taxonomic boundaries acceptable, especially for unpigmented D. barwelli and also for pink/grey D. japonica and blue/grey D. koreana. A checklist of moniligastrids is appended showing 22 species from China (including Hainan and Taiwan), 21 from Korea, nine from Japan and the Drawida ghilarovi Gates, 1969 species-complex from far eastern Russian (Siberia). Recent Drawida dandongensis Zhang & Sun, 2014 from Sino-Korean border is misdescribed and cannot be meaningfully compared to any other Drawidas.

• ALGAE
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• v.33 no.1
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• pp.55-68
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• 2018

Foliose species of the Bangiaceae (Porphyra s. l.) are very important in Korean fisheries, and their taxonomy and ecophysiology have received much attention because of the potential for developing or improving aquaculture techniques. Although 20 species of foliose Bangiales have been listed from the Korean coast, some of them remain uncertain and need further comparative morphological studies with molecular comparison. In this study, we confirm the distribution of four Pyropia species from the east coast of Korea, Pyropia kinositae, P. moriensis, P. onoi, and P. retorta sp. nov., based on morphology and rbcL sequence data. Although P. onoi was listed in North Korea in old floral works, its occurrence on the east coast of South Korea is first revealed in this study based on molecular data. P. kinositae and P. moriensis, which were originally described from Hokkaido, Japan, are first reported on the east coast of Korea in this study. Pyropia retorta sp. nov. and P. yezonesis share a similar thallus color and narrow spermatangial patches in the upper portion of the frond, and they have a sympatric distribution. However, P. retorta can be distinguished by the curled or twisted thalli and by molecular data. The biogeographic pattern of the two native species, P. kinositae and P. retorta, suggests that the east coast of Korea may have been a place of refugia during the Last Glacial Maximum (LGM), and then recolonized to the northern part of Japan through the restored East Korean Warm Current after the LGM.

• Mycobiology
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• v.44 no.3
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• pp.121-130
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• 2016

Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade.

• Korean Journal of Ichthyology
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• v.18 no.4
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• pp.293-299
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• 2006

Copper,zinc superoxide dismutase (Cu,Zn-SOD) plays a key role to the first antioxidant defense system against oxidative stress in diverse aerobic organisms. Due to the housekeeping action of Cu,Zn-SOD, it was reported that the structure and function have been conserved during evolution. In this study Cu,Zn-SOD from cloudy catshark Scyliorhinus torazame was subjected to phylogenetic analyses to know its evolutionary relationship in the vertebrate lineage. Molecular phylogenetic trees inferred by NJ, MP, ML and/or Bayesian analyses showed two shark species, Prionace glauca and S. torazame grouped together with high statistical supports. In general, they placed at the separated position from bony vertebrates. Thereafter, bony vertebrates composed of teleosts and birds/mammals (amniotes) formed a monophyletic group. Each teleost and amniote clade was also supported by relatively high statistical values. These phylogenetic relationships are well congruent with the phylogenetic hypothesis of the ancestral position of cartilaginous fishes to bony vertebrates.

• ALGAE
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• v.30 no.1
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• pp.1-13
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• 2015

A new macroscopic riverine red algal species, Lemanea manipurensis sp. nov. (Batrachospermales) is described from Manipur in northeast India. It has a sparsely branched, pseudoparenchymatous thallus with a single, central axial filament that lacks cortical filaments. Spermatangia occur generally in isolated, low and indistinct patches or form an almost continuous ring around the axis. Carposporophytes project into the hollow thallus cavity without an ostiole. The most striking morphological feature is the carposporophyte with very short gonimoblast filaments having cylindrical, narrow and sparsely branched sterile filaments, the terminal cell of each branch with a single, large, elongate carpospore. The widely distributed L. fluviatilis has spherical carpospores in long branched chains. Phylogenetic analysis of rbcL sequence data and comparison with other Batrachospermales clearly show that our specimens do not align with other species of Lemanea and Paralemanea investigated thus far. Five specific names attributed in previous literature (1973-2014) to Lemanea from Manipur, L. australis, L. catenata, L. fluviatilis, L. mamillosa, and L. torulosa are rejected until critical anatomical and molecular evidence is available for specimens from the Manipur river systems. Taxa referable to Paralemanea were not confirmed for India in this study. In view of the high demand for food and medical uses of L. manipurensis in northeast India, conservation measures are needed for its long term survival. The present paper constitutes the first combined morphological / molecular study on a freshwater red alga from India.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.10
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• pp.1566-1572
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• 2020

Objective: The extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China. Methods: In the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds. Results: Twenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious. Conclusion: The genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.

• ALGAE
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• v.31 no.3
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• pp.205-217
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• 2016

Freshwater red tides due to dinoflagellates have caused spectacular and regular “summer reddening” in recent years in Baishihai Lake, a temperate, meromictic, meso- or oligotrophic, high-altitude, landslide-dammed, deep lake located at the eastern edge of Tibetan Plateau in China. Based on morphological and molecular analyses, the causative organism has been identified as a new woloszynskioid dinoflagellate, Tovellia diexiensis Q. Zhang et G. X. Liu sp. nov. The vegetative cells are 20-32 μm long and 16-24 μm wide. They have a hemispherical episome and a broadly rounded hyposome with a short characteristic antapical spine. Usually cells are bright red due to the presence of numerous red-pigmented bodies, which often masked the yellowish green discoid chloroplasts. The amphiesma of motile cells comprise mainly quadrilateral, pentagonal or hexagonal thin plates, arranged in 4-5 latitudinal series on the episome, 1 in the cingulum and 4 on the hyposome. Molecular phylogenies based on small subunit ribosomal DNA and large subunit ribosomal DNA (LSU) indicate T. diexiensis from Baishihai Lake to belong to the family Tovelliaceae, which was monophyletic in our LSU phylogenies. During the bloom-forming period in 2005, cell density of T. diexiensis reached 9.15 × 10⁵ cells L⁻¹. Astaxanthin and its diester were found to be the major pigments in T. diexiensis, resulting in a characteristic blood-red color of the water in Baishihai Lake.