• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1411-1422
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• 2021

Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host's evolutionary adaptation process.

• The Plant Pathology Journal
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• v.37 no.3
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• pp.258-267
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• 2021

Asian pear (Pyrus pyrifolia) is a widely cultivated and commercially important fruit crop, which is occasionally subject to severe economic losses due to latent viral infections. Thus, the aim of the present study was to examine and provide a comprehensive overview of virus populations infecting a major pear cultivar ('Singo') in Korea. From June 2017 to October 2019, leaf samples (n = 110) of pear trees from 35 orchards in five major pear-producing regions were collected and subjected to RNA sequencing. Most virus-associated contigs matched the sequences of known viruses, including apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV). However, some contigs matched the sequences of apple green crinkle-associated virus and cucumber mosaic virus. In addition, three complete or nearly complete genomes were constructed based on transcriptome data and subjected to phylogenetic analyses. Based on the number of virus-associated reads, ASGV and ASPV were identified as the dominant viruses of 'Singo.' The present study describes the virome of a major pear cultivar in Korea, and looks into the diversity of viral communities in this cultivar. This study can provide valuable information on the complexity of genetic variability of viruses infecting pear trees.

• Journal of Animal Science and Technology
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• v.65 no.3
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• pp.679-682
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• 2023

The Lactococcus taiwanensis strain K_LL004 was isolated from the gut of a grasshopper (Oxya chinensis sinuosa) collected from local farm in Korea. L. taiwanensis strain K_LL004 is the functional probiotic candidate with an ability to hydrolyse plant polysaccharides. The complete genome of the L. taiwanensis strain K_LL004 contains one circular chromosome (1,995,099 bp) with a guanine + cytosine (GC) content of 38.8%. Moreover, 1,929 Protein-coding sequence, 19 rRNA genes, and 62 tRNA genes were identified based on results of annotation. L. taiwanensis strain K_LL004 has a gene, which encodes hydrolytic enzymes such as beta-glucosidase and beta-xylosidase, that hydrolyzes plant polysaccharides.

• Genomics & Informatics
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• v.6 no.4
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• pp.161-165
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• 2008

In 2008 at least five complete genome sequences are available. It is known that there are over 15,000,000 genetic variants, called SNPs, in the dbSNP database. The cost of full genome sequencing in 2009 is claimed to be less than $5000 USD. The genomics era has arrived in 2008. This review introduces technologies, bioinformatics, genomics visions, and variomics projects. Variomics is the study of the total genetic variation in an individual and populations. Research on genetic variation is the most valuable among many genomics research branches. Genomics and variomics projects will change biology and the society so dramatically that biology will become an everyday technology like personal computers and the internet. 'BioRevolution' is the term that can adequately describe this change.

• Journal of Plant Biotechnology
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• v.45 no.3
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• pp.207-216
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• 2018

Solanum berthaultii is one of the wild diploid Solanum species, which is an excellent resource in potato breeding owing to its resistance to several important pathogens. On the other hand, sexual hybridization between S. berthaultii and S. tuberosum (potato) is limited because of their sexual incompatibility. Therefore, cell fusion can be used to introgress various novel traits from this wild species into the cultivated potatoes. After cell fusion, it is crucial to identify fusion products with the aid of molecular markers. In this study, the chloroplast genome sequence of S. berthaultii obtained by next-generation sequencing technology was described and compared with those of five other Solanum species to develop S. berthaultii specific markers. A total sequence length of the chloroplast genome is 155,533 bp. The structural organization of the chloroplast genome is similar to those of the five other Solanum species. Phylogenic analysis with 25 other Solanaceae species revealed that S. berthaultii is most closely located with S. tuberosum. Additional comparison of the chloroplast genome sequence with those of the five Solanum species revealed 25 SNPs specific to S. berthaultii. Based on these SNPs, six PCR-based markers for differentiating S. berthaultii from other Solanum species were developed. These markers will facilitate the selection of fusion products and accelerate potato breeding using S. berthaultii.

• Korean Journal of Microbiology
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• v.53 no.1
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• pp.67-69
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• 2017

Complete genome sequences were retrieved from the strain RR3-28 that was isolated from a seawater recirculating aquaculture system and related to the genus Nitratireductor. The genome sequence consists of a single, circular chromosome of 3,357,577 bp with 58.6% G+C content. The genome was identified to contain twenty-one genes related to denitrification and one intact prophage.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2002.09a
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• pp.193-193
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• 2002

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.64-64
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• 2018

The genus Cenchrus (Poaceae), containing ca. 97 species, is distributed throughout Australia, Africa and Indian sub-continent and which was introduced to the United States and Mexico for use in improved pasture. In Korea, especially Daecheong Island, it is one of the most hazardous invasive plant, which causes serious environmental threats, biodiversity damages and physically negative impact on humans and animals. It can cause serious damage to farms, fields and white sand beaches. However, the chloroplast (cp) genome sequences and information of Cenchrus longispinus have been not addressed, so we provide the complete cp genome of Cenchrus longispinus using next-generation sequencing technology. The size of cp genomes of this Daecheong Island species (Cenchrus longispinus) is 137,144 bp, and it shows a typical quadripartite structure. Consisting of the large single copy (LSC; 80,223 bp), small single copy (SSC; 12,449 bp), separated by a pair of inverted repeats (IRs; 22,236 bp). This cp genome contains 75 unique genes, 4 rRNA coding genes, 33 tRNA coding genes and 21 duplicated in the IR regions, with the gene content and organization are similar to other Poaceae cp genomes. Our comparative analysis identified four cpDNA regions (rpl16, rbcL, ndhH and ndhF) from three Cenchrus species, two Setaria species and one Pennisetum species which may be useful for molecular identification.

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.157-159
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• 2019

Pseudomonas fluorescens NBC275 (Pf275) isolated from soil sample collected at riverside of Nakdonggang showed antagonistic activity against fungal pathogens of plants and insects. Here we present complete genome sequence of Pf275. The genome comprises of 6,610,362 bp with GC content of 60.9%, which includes 5,869 predicted protein-coding genes, 16 rRNAs, and 65 tRNAs. Genome analysis revealed gene clusters encoding antimicrobial secondary metabolites such as pyoverdine, 2, 4-diacetylphloroglucinol, and phenazine, which are known to play essential roles in biocontrol of diseases.

• The Plant Pathology Journal
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• v.37 no.2
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• pp.162-172
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• 2021

Soybean mosaic virus (SMV) is the predominant viral pathogen that affects the yield and quality of soybean. The natural host range for SMV is very narrow, and generally limited to Leguminosae. However, we found that SMV can naturally infect Pinellia ternata and Atractylodes macrocephala. In order to clarify the molecular mechanisms underlying the cross-family infection of SMV, we used double-stranded RNA extraction, rapid amplification of cDNA ends polymerase chain reaction and Gibson assembly techniques to carry out SMV full-length genome amplification from susceptible soybeans and constructed an infectious cDNA clone for SMV. The genome of the SMV Shanxi isolate (SMV-SX) consists of 9,587 nt and encodes a polyprotein consisting of 3,067 aa. SMV-SX and SMV-XFQ008 had the highest nucleotide and amino acid sequence identities of 97.03% and 98.50%, respectively. A phylogenetic tree indicated that SMV-SX and SMV-XFQ018 were clustered together, sharing the closest relationship. We then constructed a pSMV-SX infectious cDNA clone by Gibson assembly technology and used this clone to inoculate soybean and Ailanthus altissima; the symptoms of these hosts were similar to those caused by the virus isolated from natural infected plant tissue. This method of construction not only makes up for the time-consuming and laborious defect of traditional methods used to construct infectious cDNA clones, but also avoids the toxicity of the Potyvirus special sequence to Escherichia coli, thus providing a useful cloning strategy for the construction of infectious cDNA clones for other viruses and laying down a foundation for the further investigation of SMV cross-family infection mechanisms.