• The Plant Pathology Journal
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• v.34 no.6
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• pp.514-531
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• 2018

Tomato spotted wilt virus (TSWV; Genus Orthotospovirus: Family Tospoviridae) is one of the most destructive viruses affecting a wide range of horticultural crops on a worldwide basis. In 2015 and 2016, 171 leaf and fruit samples from tomato (Solanum lycopersicum) plants with viral symptoms were collected from the fields in various regions of Iran. ELISA test revealed that the samples were infected by TSWV. The results of RT-PCR showed that the expected DNA fragments of about 819 bp in length were amplified using a pair of universal primer corresponding to the RNA polymerase gene and DNA fragments of ca 777 bp and 724 bp in length were amplified using specific primers that have been designed based on the nucleocapsid (N) and non-structural (NSs) genes, respectively. The amplified fragments were cloned into pTG19-T and sequenced. Sequence comparisons with those available in the GenBank showed that the sequences belong to TSWV. The high nucleotide identity and similarities of new sequences based on the L, N, and NSs genes showed that minor evolutionary differences exist amongst the isolates. The phylogenetic tree grouped all isolates six clades based on N and NSs genes. Phylogenetic analysis showed that the Iranian isolates were composed a new distinct clade based on a part of polymerase, N and NSs genes. To our knowledge, this is the first detailed study on molecular characterization and genetic diversity of TSWV isolates from tomato in Iran that could be known as new clade of TSWV isolates.

• Korean Journal of Agricultural Science
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• v.45 no.4
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• pp.655-663
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• 2018

The insect gut microbiome is known to have important roles in host growth, development, digestion, and resistance against pathogens. In addition, the genetic diversity of the insect gut microbiota has recently been recognized as potential genetic resources for industrial bioprocessing. However, there is limited information regarding the insect gut microbiota to better help us understand their potential benefits for enhanced pig production. With the development of next-generation sequencing methods, whole genome sequence analysis has become possible beyond traditional culture-independent methods. This improvement makes it possible to identify and characterize bacteria that are not cultured and located in various environments including the gastrointestinal tract. Insect intestinal microorganisms are known to have an important role in host growth, digestion, and immunity. These gut microbiota have recently been recognized as potential genetic resources for livestock farming which is using the functions of living organisms to integrate them into animal science. The purpose of this literature review is to emphasize the necessity of research on insect gut microbiota and their applicability to pig production or bioindustry. In conclusion, bacterial metabolism of feed in the gut is often significant for the nutrition intake of animals, and the insect gut microbiome has potential to be used as feed additives for enhanced pig performance. The exploration of the structure and function of the insect gut microbiota needs further investigation for their potential use in the swine industry particularly for the improvement of growth performance and overall health status of pigs.

• Parasites, Hosts and Diseases
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• v.56 no.6
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• pp.559-565
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• 2018

The identification and characterization of pathogenic and zoonotic tick-borne diseases like granulocytic anaplasmosis are essential for developing effective control programs. The differential diagnosis of pathogenic Anaplasma phagocytophilum and non-pathogenic A. phagocytophilum-like Anaplasma spp. is important for implementing effective treatment from control programs. The objective of the present study was to investigate the prevalence of Anaplasma spp. in horses in Korea by nucleotide sequencing and restriction enzyme fragment length polymorphism assay. Of the 627 horses included in the study, only 1 (0.2%) was infected with A. phagocytophilum. Co-infection with A. phagocytophilumlike Anaplasma spp. was not detected in the study. The 16S rRNA sequence of A. phagocytophilum was similar (99.5-100%) to A. phagocytophilum 16S rRNA isolated from horses in other countries. PCR adapted to amplify A. phagocytophilum groEL and msp2 genes failed to generate amplicons, suggesting genetic diversity in these genes. This study is the first molecular detection of A. phagocytophilum in horses in Korea. Human granulocytic anaplasmosis and animal infection of A. phagocytophilum have been reported in Korea recently. Because of vector tick distribution, global warming, and the increase of the horse industry, horses should be considered as a potential reservoir for A. phagocytophilum, and cross infectivity should be evaluated even though a low prevalence of infection was detected in this study. Furthermore, continuous surveillance and effective control measures for A. phagocytophilum should be established to prevent disease distribution and possible transmission to humans.

• Journal of Microbiology and Biotechnology
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• v.29 no.9
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• pp.1391-1400
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• 2019

Canine parvoviral enteritis (PVE) is an important intestinal disease of the puppies; however, the potential impact of the canine parvovirus (CPV) on the gut microbiota has not been investigated. Therefore, the aim of this study was to evaluate the gut microbial shifts in puppies naturally infected with CPV. Fecal samples were collected from healthy dogs and those diagnosed with PVE at 4, 6, 8, and 12 weeks of age. The distal gut microbiota of dogs was characterized using Illumina MiSeq sequencing of the bacterial 16S rRNA genes. The sequence data were analyzed using QIIME with an Operational Taxonomic Unit definition at a similarity cutoff of 97%. Our results showed that the CPV was associated with significant microbial dysbiosis of the intestinal microbiota. Alpha diversity and species richness and evenness in dogs with PVE decreased compared to those of healthy dogs. At the phylum level, the proportion of Proteobacteria was significantly enriched in dogs with PVE while Bacteroidetes was significantly more abundant in healthy dogs (p < 0.05). In dogs with PVE, Enterobacteriaceae was the most abundant bacterial family accounting for 36.44% of the total bacterial population compared to only 0.21% in healthy puppies. The two most abundant genera in healthy dogs were Prevotella and Lactobacillus and their abundance was significantly higher compared to that of dogs with PVE (p < 0.05). These observations suggest that disturbances of gut microbial communities were associated with PVE in young dogs. Evaluation of the roles of these bacterial groups in the pathophysiology of PVE warrants further studies.

• Molecules and Cells
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• v.42 no.9
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• pp.637-645
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• 2019

Effector-triggered immunity (ETI) is an effective layer of plant defense initiated upon recognition of avirulence (Avr) effectors from pathogens by cognate plant disease resistance (R) proteins. In rice, a large number of R genes have been characterized from various cultivars and have greatly contributed to breeding programs to improve resistance against the rice blast pathogen Magnaporthe oryzae. The extreme diversity of R gene repertoires is thought to be a result of co-evolutionary history between rice and its pathogens including M. oryzae. Here we show that Pii is an allele of Pi5 by DNA sequence characterization and complementation analysis. Pii-1 and Pii-2 cDNAs were cloned by reverse transcription polymerase chain reaction from the Pii-carrying cultivar Fujisaka5. The complementation test in susceptible rice cultivar Dongjin demonstrated that the rice blast resistance mediated by Pii, similar to Pi5, requires the presence of two nucleotide-binding leucine-rich repeat genes, Pii-1 and Pii-2. Consistent with our hypothesis that Pi5 and Pii are functionally indistinguishable, the replacement of Pii-1 by Pi5-1 and Pii-2 by Pi5-2, respectively, does not change the level of disease resistance to M. oryzae carrying AVR-Pii. Surprisingly, Exo70F3, required for Pii-mediated resistance, is dispensable for Pi5-mediated resistance. Based on our results, despite similarities observed between Pi5 and Pii, we hypothesize that Pi5 and Pii pairs require partially distinct mechanisms to function.

• Molecules and Cells
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• v.42 no.1
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• pp.56-66
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• 2019

Histidine triad nucleotide-binding protein (HINT) is a member of the histidine triad (HIT) superfamily, which has hydrolase activity owing to a histidine triad motif. The HIT superfamily can be divided to five classes with functions in galactose metabolism, DNA repair, and tumor suppression. HINTs are highly conserved from archaea to humans and function as tumor suppressors, translation regulators, and neuropathy inhibitors. Although the structures of HINT proteins from various species have been reported, limited structural information is available for fungal species. Here, to elucidate the structural features and functional diversity of HINTs, we determined the crystal structure of HINT from the pathogenic fungus Candida albicans (CaHINT) in complex with zinc ions at a resolution of $2.5{\AA}$. Based on structural comparisons, the monomer of CaHINT overlaid best with HINT protein from the protozoal species Leishmania major. Additionally, structural comparisons with human HINT revealed an additional helix at the C-terminus of CaHINT. Interestingly, the extended C-terminal helix interacted with the N-terminal loop (${\alpha}1-{\beta}1$) and with the ${\alpha}3$ helix, which appeared to stabilize the dimerization of CaHINT. In the C-terminal region, structural and sequence comparisons showed strong relationships among 19 diverse species from archea to humans, suggesting early separation in the course of evolution. Further studies are required to address the functional significance of variations in the C-terminal region. This structural analysis of CaHINT provided important insights into the molecular aspects of evolution within the HIT superfamily.

• Parasites, Hosts and Diseases
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• v.58 no.6
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• pp.681-687
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• 2020

Giardia lamblia is a common enteric pathogen associated with diarrheal diseases. There are some reports of G. lamblia infection among different breeds of cattle in recent years worldwide. However, it is yet to know whether cattle in Jiangxi province, southeastern China is infected with G. lamblia. The objectives of the present study were to investigate the prevalence and examine the multilocus genotypes of G. lamblia in cattle in Jiangxi province. A total of 556 fecal samples were collected from 3 cattle breeds (dairy cattle, beef cattle, and buffalo) in Jiangxi province, and the prevalence and genotypes of G. lamblia were determined by the nested PCR amplification of the beta-giardin (bg) gene. A total of 52 samples (9.2%) were positive for G. lamblia. The highest prevalence of G. lamblia was detected in dairy cattle (20.0%), followed by that in beef cattle (6.4%), and meat buffalo (0.9%). Multilocus sequence typing of G. lamblia was performed based on sequences of the bg, triose phosphate isomerase and glutamate dehydrogenase loci, and 22, 42, and 52 samples were amplifiable, respectively, forming 15 MLGs. Moreover, one mixed G. lamblia infection (assemblages A and E) was found in the present study. Altogether, 6 novel assemblage E subtypes (E41*-E46*) were identified for the first time. These results not only provided baseline data for the control of G. lamblia infection in cattle in this southeastern province of China, but also enriched the molecular epidemiological data and genetic diversity of G. lamblia in cattle.

• Journal of Species Research
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• v.11 no.4
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• pp.266-277
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• 2022

The current surveys of Ulva in the subtidal area around Jeju Island give a chance to discover unrecorded green algal species of the Korean macroalgal flora. As a result of this investigation, we found Ulva adhaerens Matusmoto & Shimada, inhabiting the subtidal regions, up to 15 m deep, and conducted the DNA barcoding on plastid rbcL-3P and tufA regions with describing the morphological characteristics. Our specimens of U. adhaerens forms a monophyletic clade with the Japanese type specimen and U. piritoka Ngāti Kuri, Heesch & W.A. Nelson from New Zealand exhibiting each 0.3% sequence divergences, respectively, in the plastid rbcL-3P. The genetic variation of U. adhaerens clade is 1.0-3.9% in rbcL-3P and 4.8-9.8% in tufA to each Ulva species, including the generic type, U. lactuca Linneaus. The morphology of Korean U. adhaerens specimens is identical to the type specimens of U. adhaerens from Japan having the development of rhizoidal filaments from both of the cell layers of the distromatic blade and the extension of rhizoidal clumps with adhesive trait between blades by extended rhizoidal clumps at the basal blades. The thallus attachment to substrate is by numerous minute discoidal plates made up of rhizoids originating from the inner part of distromatic blades in basal. Although there are still some problems to resolve the relationship between U. adhaerens and U. piritoka in the rbcL dataset and the phylogenetic pattern of the Group II intron of rbcL, we propose the new record of U. adhaerens in Korean macroalgal flora based on the morphological characteristics of Korean specimens. Continued study of the genus Ulva by morphological and molecular assessment will delimit the species of Ulva, elucidate the relationships between them, and uncover the species diversity.

• Journal of Species Research
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• v.11 no.3
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• pp.133-142
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• 2022

In 2020, 24 bacterial strains were isolated from algae, kudzu leaf, mud, pine cone, seashore sand, sea water, soil, tidal flat, and wetland from the Republic of Korea. Isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species, but not reported in Korea, were highlighted as unrecorded species. These isolates were allocated to the phyla Bacteroidetes and Proteobacteria as unrecorded species in Korea. The four Bacteroidetes strains were classified into the families Chitinophagaceae, Flavobacteriaceae, and Sphingobacteriaceae (of the orders Chitinophagales, Flavobacteriales, and Sphingobacteriales, respectively). The 20 Proteobacteria strains belonged to the Aeromonadaceae, Marinobacter, Microbulbiferaceae, Enterobacteriaceae, Erwiniaceae, Morganellaceae, Yersiniaceae, Lysobacteraceae, Halomonadaceae, Moraxellaceae, Pseudomonadaceae, Steroidobacteraceae, Xanthomonadaceae, and Myxococcaceae (of the orders Aeromonadales, Alteromonadales, Cellvibrionales, Enterobacterales, Lysobacterales, Oceanospirillales, Pseudomonadales, Steroidobacter, Xanthomonadales, and Myxococcales). This study focused on the description of 24 unreported bacterial species in Korea in the phyla Bacteroidetes and Proteobacteria belonging to six classes.

• ALGAE
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• v.37 no.1
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• pp.1-14
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• 2022

Cyanobacteria are distributed worldwide, and many new cyanobacterial species are discovered in tropical region. The Nostoc-like genus Amazonocrinis has been separated from the genus Nostoc based on polyphasic methods. However, species diversity within this genus remains poorly understood systematically because only one species (Amazonocrinis nigriterrae) has been described. In this study, two novel strains (NUACC02 and NUACC03) were isolated from moist rice field soil in Thailand. These two strains were characterized using a polyphasic approach, based on morphology, 16S rRNA phylogenetic analysis, internal transcribed spacer secondary structure and ecology. Phylogenetic analyses based on 16S rRNA gene sequences confirmed that the two novel strains formed a monophyletic clade related to the genus Amazonocrinis and were distant from the type species A. nigriterrae. The 16S rRNA gene sequence similarity (<98.1%) between novel strains and all other closely related taxa including the Amazonocrinis members exceeded the cutoff for species delimitation in bacteriology, reinforcing the presence of a new Amazonocrinis species. Furthermore, the novel strains possessed unique phenotypic characteristics such as the presence of the sheath, necridia-like cells, larger cell dimension and akinete cell arrangement in long-chains and the singularity of D1-D1', Box-B, V2, and V3 secondary structures that distinguished them from other Amazonocrinis members. Considering all the results, we described our two strains as Amazonocrinis thailandica sp. nov. in accordance with the International Code of Nomenclature for Algae, Fungi and Plants.