• Journal of Life Science
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• v.33 no.8
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• pp.605-611
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• 2023

Recently, sporadic cases of human infection by genetic reassortants of H7Nx influenza A viruses have been reported; such viruses have also been continuously isolated from avian species. In this study, A/wild bird/South Korea/sw-anu/2023, a novel reassortant of the H7N1 avian influenza virus, was analyzed using full-genome sequencing and molecular characterization. Phylogenetic analysis showed that A/wild bird/South Korea/sw-anu/2023 belonged to the Eurasian lineage of H7Nx viruses. The polymerase basic (PB)2, PB1, polymerase acidic (PA), and nucleoprotein (NP) genes of these viruses were found to be closely related to those of avian influenza viruses isolated from wild birds, while the hemagglutinin (HA), neuraminidase (NA), matrix (M), and nonstructural (NS) genes were similar to those of avian influenza viruses isolated from domestic ducks. In addition, A/wild bird/South Korea/sw-anu/2023 also had a high binding preference for avian-specific glycans in the solid-phase direct binding assay. These results suggest the presence of a new generation of H7N1 avian influenza viruses in wild birds and highlight the reassortment of avian influenza viruses found along the East Asian-Australasian flyway. Overall, H7Nx viruses circulate worldwide, and mutated H7N1 avian viruses may infect humans, which emphasizes the requirement for continued surveillance of the H7N1 avian influenza virus in wild birds and poultry.

• Research in Plant Disease
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• v.29 no.1
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• pp.79-81
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• 2023

During the nationwide survey of fire blight, the typical shoot blight symptoms were found on Korean mountain ash (Sorbus alnifolia) which was located near an orchard that produced fire blight on pear trees in Eumseong, Korea, May 2021. To identify the causal agent, we progressed isolation from the symptomatic leaves and shoots. Two white and mucoid colonies were isolated into the pure culture. Two isolates were identified as Erwinia amylovora according to the colony-polymerase chain reaction (PCR) with amsB primers and the phylogenetic tree using 16S rRNA sequences. To test of pathogenicity of two isolates, we inoculated immature pear fruits and understock of apple. We observed necrosis and oozes on immature pear fruits and shoot blight resulting in necrosis on apple shoots six days after inoculation. Colonies were recovered from the inoculated pears and apples, and identity was confirmed through colony PCR for amsB genes. To our knowledge, E. amylovora was first reported on Korean mountain ash native to South Korea.

• Journal of Microbiology and Biotechnology
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• v.33 no.2
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• pp.188-194
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• 2023

Microbacterium elymi KUDC0405^T was isolated from the rhizosphere of Elymus tsukushiensis from the Dokdo Islands. The KUDC0405^T strain was Gram-stain-positive, non-spore forming, non-motile, and facultatively anaerobic bacteria. Strain KUDC0405^T was a rod-shaped bacterium with size dimensions of 0.3-0.4 × 0.7-0.8 ㎛. Based on 16S rRNA gene sequences, KUDC0405^T was most closely related to Microbacterium bovistercoris NEAU-LLE^T (97.8%) and Microbacterium pseudoresistens CC-5209^T (97.6%). The dDDH (digital DNA-DNA hybridization) values between KUDC0405^T and M. bovistercoris NEAU-LLE^T and M. pseudoresistens CC-5209^T were below 17.3% and 17.5%, respectively. The ANI (average nucleotide identity) values among strains KUDC0405^T, M. bovistercoris NEAU-LLE^T, and M. pseudoresistens CC-5209^T were 86.6% and 80.7%, respectively. The AAI (average amino acid identity) values were 64.66% and 64.97%, respectively, between KUDC0405^T and its closest related type strains. The genome contained 3,596 CDCs, three rRNAs, 46 tRNAs, and three non-coding RNAs (ncRNAs). The genomic DNA GC content was 70.4%. The polar lipids included diphosphatydilglycerol, glycolipid, phosphatydilglycerol, and unknown phospholipid, and the major fatty acids were anteiso-C_17:0 and iso-C_16:0. Strain KUDC0405^T contained MK-12 as the major menaquinone. Based on genotypic, phylogenetic, and phenotypic properties, strain KUDC0405^T should be considered a novel species within the genus Microbacterium, for which we propose the name M. elymi sp. nov., and the type strain as KUDC0405^T (=KCTC 49411^T, =CGMCC1.18472^T).

• Research in Plant Disease
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• v.28 no.4
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• pp.231-236
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• 2022

Oxypetalum coeruleum, commonly known as Tweedia, is a perennial herbaceous plant of the Apocynaceae family native to southern Brazil and Uruguay. Tweedia plants are grown as one of the most popular ornamental flowers for floral arrangement in Korea. In May 2021, several tweedia plants in a single greenhouse in Gimje, Jeollabuk-do were found to show virus-like symptoms including necrotic rings, vein-clearing, chlorotic mottle, and mosaic on the leaves, and necrosis on the stems. Here, we have identified tomato spotted wilt virus (TSWV) in symptomatic tweedia leaves by applying high-throughput RNA sequencing. In the result, a single infection by TSWV was verified without mixed infections of different virus species. To confirm the presence of TSWV, a reverse transcription polymerase chain reaction was performed with a specific primer set to the N gene of TSWV. The complete genomic sequence of L, M, and S segments of TSWV 'Oxy' isolate were determined and deposited in GenBank under accession numbers LC671525, LC671638, and LC671639, respectively. In the phylogenetic tree analysis by maximum likelihood method, 'Oxy' isolate showed a high relationship with TSWV 'Gumi' isolate from Gerbera jamesonii in Gyeongsangbuk-do, Korea; for all three RNA segments. To our knowledge, this is the first report of TSWV infection of O. coeruleum in Korea.

• Animal Bioscience
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• v.36 no.4
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• pp.570-583
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• 2023

Objective: Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens. Methods: Chicken FGFs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the FGFs genes in different chicken tissues were obtained from the genome-wide RNA-seq. Results: A total of 20 FGF genes were identified in the chicken genome, which were classified into seven distinct groups (A-F) in the phylogenetic tree. Gene structure analysis revealed that members of the same clade had the same or similar exon-intron structure. Chromosome mapping suggested that FGF genes were widely dispersed across the chicken genome and were located on chromosomes 1, 4-6, 9-10, 13, 15, 28, and Z. In addition, the interactions among FGF proteins and between FGFs and mitogen-activated protein kinase (MAPK) proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. Kyoto encyclopedia of genes and genomes pathway analysis showed that FGF gene interacts with MAPK genes and are involved in stimulating signaling pathway and regulating immune responses. Furthermore, this study identified 15 differentially expressed genes (DEG) in 21 different growth stages during early chicken embryo development. RNA-sequencing data identified the DEG of FGFs on 1- and 3-days post infection in two indigenous Ri chicken lines infected with the highly pathogenic avian influenza virus H5N1 (HPAIV). Finally, all the genes examined through quantitative real-time polymerase chain reaction and RNA-Seq analyses showed similar responses to HPAIV infection in indigenous Ri chicken lines (R² = 0.92-0.95, p<0.01). Conclusion: This study provides significant insights into the potential functions of FGFs in chickens, including the regulation of MAPK signaling pathways and the immune response of chickens to HPAIV infections.

• Animal Bioscience
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• v.36 no.7
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• pp.991-1002
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• 2023

Objective: This study aimed to elucidate the underlying gene regions responsible for productive, phenotypic or adaptive traits in different ecological types of Tibetan sheep and the discovery of important genes encoding valuable traits. Methods: We used whole-genome resequencing to explore the genetic relationships, phylogenetic tree, and population genetic structure analysis. In addition, we identified 28 representative Tibetan sheep single-nucleotide polymorphisms (SNPs) and genomic selective sweep regions with different traits in Tibetan sheep by fixation index (Fst) and the nucleotide diversity (θπ) ratio. Results: The genetic relationships analysis showed that each breed partitioned into its own clades and had close genetic relationships. We also identified many potential breed-specific selective sweep regions, including genes associated with hypoxic adaptability (MTOR, TRHDE, PDK1, PTPN9, TMTC2, SOX9, EPAS1, PDGFD, SOCS3, TGFBR3), coat color (MITF, MC1R, ERCC2, TCF25, ITCH, TYR, RALY, KIT), wool traits (COL4A2, ERC2, NOTCH2, ROCK1, FGF5, SOX9), and horn phenotypes (RXFP2). In particular, a horn-related gene, RXFP2, showed the four most significantly associated SNP loci (g. 29481646 A>G, g. 29469024 T>C, g. 29462010 C>T, g. 29461968 C>T) and haplotypes. Conclusion: This finding demonstrates the potential for genetic markers in future molecular breeding programs to improve selection for horn phenotypes. The results will facilitate the understanding of the genetic basis of production and adaptive unique traits in Chinese indigenous Tibetan sheep taxa and offer a reference for the molecular breeding of Tibetan sheep.

• Korean Journal of Environmental Biology
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• v.40 no.3
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• pp.290-300
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• 2022

A strain of Alexandrium species was established by isolating cells from Jangmok Bay, Korea. Its morphology and molecular phylogeny based on LSU rRNA gene sequences were examined. In addition, growth responses of this Alexandrium species to changes in temperature, salinity, and nutrient concentrations were investigated. This Alexandrium species from Jangmok Bay had a ventral pore on the 1', which was morphologically consistent with previously described Alexandrium tamarense and A. catenella. Phylogenetic analyses revealed that this isolate was assigned to A. pacificum (Group IV) within A. tamarense species complex. In growth experiments, relatively high growth rates and cell densities of A. pacificum (Group IV) were observed at 15℃ and 20℃. This species also grew under a wide range of salinity. This indicates that this Korean isolate of A. pacificum (Group IV) is a stenothermic and euryhaline species. In growth responses to changes in nutrient levels, enhanced growth rates and cell densities of A. pacificum(Group IV) were observed with additions of nitrate and phosphate. In particular, rapid uptakes of phosphate by A. pacificum (Group IV) were observed in experimental treatments, indicating that the increase in phosphate concentration could stimulate the growth of A. pacificum(Group IV).

• Korean Journal of Environmental Biology
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• v.40 no.4
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• pp.387-397
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• 2022

The germination characteristics of the resting cysts of Pheopolykrikos hartmannii collected from the southern coastal sediments of Korea were studied at different temperature conditions, and the morphology and phylogeny of the germlings were examined. The resting cysts of Ph. hartmannii were round and characterized by a red accumulation body and many arrow-like spines and could germinate at temperature of 10 to 30℃. High germination rates (>90%) were observed at 15 and 20℃, indicating that the resting cysts could act as seed populations for the bloom initiation of Ph. hartmannii in Korean coastal waters in early summer or early fall. The morphology of the germlings was generally consistent with the previous description, and an apical groove characterized by a fully enclosed loop was observed. Phylogenetic analysis based on large SubUnit (LSU) rRNA gene sequences revealed that the germlings shared an identical sequence with the Korean and American isolates of Ph. hartmannii and was a sister clade of Polykrikos species.

• Journal of Marine Life Science
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• v.1 no.2
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• pp.79-87
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• 2016

Heavy metals such as cadmium (Cd) are highly toxic to aquatic organisms and human, even at trace concentration. Herein we investigated the effect of Cd on the gene expression of ATP-binding cassette (ABC) transporters and glutathione S-transferase (GST) in marine ciliate Euplotes crassus. Seven ABC transporters and one GST genes were partially cloned and sequences, and thereafter, transcriptional modulation of these genes after exposure to Cd for 8 h was investigated using quantitative real time RT- PCR (qRT-PCR). As results, sequence analysis and phylogenetic study revealed that E. crassus ABCs are likely typical ABC transports, in particular, B/C family, and GST gene may be similar to GST theta isoform. A significant increase in the expression of ABCs, except for ABCB21 was observed in a concentration dependent manner after exposure to Cd (0.1 and 0.5 mg/l) for 8 h. The GST mRNA level was the highest at 0.5 mg/l Cd and then reduced until control level. These findings suggest that ABCs and GST may be involved in a protective mechanism against Cd-mediated toxicity in E. crassus.

• Korean Journal of Ecology and Environment
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• v.56 no.2
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• pp.140-150
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• 2023

The Hangang River^* is necessary to manage the water environment of severe pollution due to the high density of residential areas, parks, and agriculture and the large population concentrated there. Benthic macroinvertebrates, such as chironomids larvae, are bioindicator species that reflect environmental changes and are crucial for water quality monitoring. In this study, we investigated morphological characteristics and molecular analysis of the chironomids larvae inhabiting the Hangang River area for water environment surveys. For this research, 20 rivers, lakes, and urban area in the Hangang River basin were selected. Chironomids larvae were collected from July to September 2022, and their appearance and characteristics were identified through morphological identification. In addition, phylogenetic analysis was performed based on the mtCOI gene sequences of the collected chironomids larvae, and identification at the genus level was confirmed. As a result, 32 species and 18 genera of 3 subfamilies of Chironomidae larvae were identified, and Stictochironomus sp. dominated most sites(6 sites). The morphological characteristics of the identified chironomids larvae, such as the mentum, ventromental plate, and antenna, were organized into table and pictorial keys, and a Bayesian inference molecular phylogeny was presented. These results provide basic morphological information for genus-level identification and can be used as fundamental information for water quality management.