• Korean Journal of Plant Taxonomy
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• v.40 no.1
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• pp.1-15
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• 2010

Recognizing a basal group in a taxon is one of the most important factors involved in understanding the evolutionary history of that group of life. Many botanists have suggested a sister to all other angiosperms to understand the origin and rapid diversification of angiosperms based on morphological and fossil evidence. Recent technical advances in molecular biology and the accumulation of molecular phylogenetic data have provided evidence of the extant basal-most angiosperm which is a sister to all other angiosperms. Although it is still arguable, most plant taxonomists agree that Amborella trichopoda Baill., a species (monotypic genus and monotypic family) distributed in New Caledonia, is a sister to all other extant angiosperms based on evidence from the following molecular approaches: 1) classical phylogenetic analyses based on multiple genes (or DNA regions), 2) analyses of a tree network of duplicated gene families, and 3) gene-structural evidence. As an alternative hypothesis with relatively minor evidence, some researchers have also suggested that Amborella and Nymphaeaceae form a clade that is a sister to all other angiosperms. Debate regarding the basal-most angiosperms is still ongoing and is currently one of the hot issues in plant evolutionary biology. We expect that sequencing of the whole genome of Amborella as an evolutionary model plant and subsequent studies based on this genome sequence will provide information regarding the origin and rapid diversification of angiosperms, which is Darwin's so called abominable mystery.

• 한국균학회소식:학술대회논문집
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• 2014.05a
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• pp.13-13
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• 2014

Two kinds of mushrooms, Gumji (金芝; Ganoderma) and Soji, were described in old book of Samguksagi (History of the three kingdoms; B.C 57~A.D 668; written by Bu Sik Kim in 1145) in Korea-dynasty. Many kinds of mushrooms were also described in more than 17 kinds of old books during Chosun-dynasty (1392~1910) in Korea. Nowadays, mushroom cultivation has been increased through out the world last decade years. Production of mushrooms has also been increased 10-20% and many varieties have been cultivated. Similar trends were also observed in Korea. Approximately two hundred commercial strains of 37 species in mushrooms were developed and distributed to cultivators. Somatic hybrid variety of oyster mushroom 'Wonhyeong-neutari' were developed by protoplast fusion, and distributed to grower in 1989. The fruiting body yield index of somatic hybrids of Pleurotus ranged between 27 and 155 compared to parental values of 100 and 138. In addition, more diverse mushroom varieties such as Phellinus baumi, Auricularia spp., Pleurotus ferulae, Hericium erinaceus, Hypsizigus marmoreus, Grifola frondosa, Agrocybe aegerita and Pleurotus cornucopiae have been attempted to cultivate in small scale cultivation. Production of mushrooms as food was 190,111 metric tons valued at 800 billion Korean Won (one trillion won if include mushroom factory products; 1dollar = 1,040 Won) in 2011. Major cultivated species are Pleurotus ostreatus, Pleurotus eryngii, Flammulina velutipes, Lentinula edodes, Agaricus bisporus, and Ganoderma lucidum, which cover 90% of total production. Since mushroom export was initiated from 1960 to 1980, the export and import of mushrooms have been increased in Korea. Technology developed for liquid spawn production and automatic cultivation systems lead to the reduction of the production cost resulting in the increasement of mushroom export. However some species were imported because of high production cost for these mushrooms requiring the effective cultivation methods. Developing of effective post-harvest system will be also directly related to mushroom export. In academic area, RDA scientists have been conducting mushroom genome projects. One of the main results is the whole genome sequencing of Flammulina velutipes for molecular breeding. An electrophoretic karyotype of of F. velutipes was obtained using CHEF with 7 chromosomes, with a total genome size of approximately 26.7 Mb. The mususcript of the genome of F. velutipes was published in PLOS ONE this year. For medicinal mushrooms, we have been conducting the genome research on Cordyceps and its related species for developing functional foods using this mushroom. In 2013, Korea Food and Drug Administraion (KFDA) approved Cordyceps mushroom for its value as an immune booster.

• Journal of Marine Life Science
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• v.6 no.2
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• pp.97-105
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• 2021

Tegillarca granosa, is one of the most important fishery resources throughout Asia. However, due to industrialization factories, marine environmental pollution, and global warming, the marine fishery production has drop sharply. In order to understand the genetic factors of the blood clam, which is a major fishery resource on the southern coast of Korea, the whole genome of blood clam was studied. The assembled genome of T. granosa was 915.4 Mb, and 19 chromosomes were identified. 25,134 genes were identified, and 22,745 genes were functionally annotated. As a result of performing gene gain and loss analysis between the blood clam genome and eight other types of shellfish, it was confirmed that 725 gene groups were expanded, and 479 gene groups were contracted. The homeobox gene cluster of blood clam showed a well-preserved genetic structure within lophotrochozoan ancestor. T. granosa genome showed high similarity between three hemoglobin genes with Scarpharca broughtonii. The blood clam genome will provide information for the genetic and physiological characteristics of blood clam adaptation, evolution, and the development of aquaculture industry.

• Journal of Microbiology and Biotechnology
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• v.30 no.4
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• pp.505-514
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• 2020

The symbiotic nature of the relationship between algae and marine bacteria is well-studied among the complex microbial interactions. The mutual profit between algae and bacteria occurs via nutrient and vitamin exchange. It is necessary to analyze the genome sequence of a bacterium to predict its symbiotic relationships. In this study, the genome of a marine bacterium, Pseudoruegeria sp. M32A2M, isolated from the south-eastern isles (GeoJe-Do) of South Korea, was sequenced and analyzed. A draft genome (91 scaffolds) of 5.5 Mb with a DNA G+C content of 62.4% was obtained. In total, 5,101 features were identified from gene annotation, and 4,927 genes were assigned to functional proteins. We also identified transcription core proteins, RNA polymerase subunits, and sigma factors. In addition, full flagella-related gene clusters involving the flagellar body, motor, regulator, and other accessory compartments were detected even though the genus Pseudoruegeria is known to comprise non-motile bacteria. Examination of annotated KEGG pathways revealed that Pseudoruegeria sp. M32A2M has the metabolic pathways for all seven vitamin Bs, including thiamin (vitamin B1), biotin (vitamin B7), and cobalamin (vitamin B12), which are necessary for symbiosis with vitamin B auxotroph algae. We also identified gene clusters for seven secondary metabolites including ectoine, homoserine lactone, beta-lactone, terpene, lasso peptide, bacteriocin, and non-ribosomal proteins.

• Journal of Microbiology and Biotechnology
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• v.30 no.7
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• pp.974-981
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• 2020

Sequence type 410 (ST410) of Escherichia coli is an extraintestinal pathogen associated with multi drug resistance. In this study, we aimed to investigate the horizontal propagation pathway of a high-risk clone of E. coli ST410 that produces Klebsiella pneumoniae carbapenemase (KPC). blaKPC-encoding E. coli and K. pneumoniae isolates were evaluated, and complete sequencing and comparative analysis of blaKPC-encoding plasmids from E. coli and K. pneumoniae, antimicrobial susceptibility tests, polymerase chain reaction, multilocus sequence typing, and conjugal transfer of plasmids were performed. Whole-genome sequencing was performed for plasmids mediating KPC-2 production in E. coli and K. pneumoniae clinical isolates. Strains E. coli CPEc171209 and K. pneumoniae CPKp171210 were identified as ST410 and ST307, respectively. CPEc171209 harbored five plasmids belonging to serotype O8:H21, which is in the antimicrobial-resistant clade C4/H24. The CPKp171210 isolate harbored three plasmids. Both strains harbored various additional antimicrobial resistance genes. The IncX3 plasmid pECBHS_9_5 harbored blaKPC-2 within a truncated Tn4401a transposon, which also contains blaSHV-182 with duplicated conjugative elements. This plasmid displayed 100% identity with the IncX3 plasmid pKPBHS_10_3 from the K. pneumoniae CPKp171210 ST307 strain. The genes responsible for the conjugal transfer of the IncX3 plasmid included tra/trb clusters and pil genes coding the type IV pilus. ST410 can be transmitted between patients, posing an elevated risk in clinical settings. The emergence of a KPC-producing E. coli strain (ST410) is concerning because the blaKPC-2-bearing plasmids may carry treatment resistance across species barriers. Transgenic translocation occurs among carbapenem-resistant bacteria, which may spread rapidly via horizontal migration.

• Journal of Ginseng Research
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• v.37 no.2
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• pp.227-247
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• 2013

MicroRNAs (miRNAs) are a class of recently discovered non-coding small RNA molecules, on average approximately 21 nucleotides in length, which underlie numerous important biological roles in gene regulation in various organisms. The miRNA database (release 18) has 18,226 miRNAs, which have been deposited from different species. Although miRNAs have been identified and validated in many plant species, no studies have been reported on discovering miRNAs in Panax ginseng Meyer, which is a traditionally known medicinal plant in oriental medicine, also known as Korean ginseng. It has triterpene ginseng saponins called ginsenosides, which are responsible for its various pharmacological activities. Predicting conserved miRNAs by homology-based analysis with available expressed sequence tag (EST) sequences can be powerful, if the species lacks whole genome sequence information. In this study by using the EST based computational approach, 69 conserved miRNAs belonging to 44 miRNA families were identified in Korean ginseng. The digital gene expression patterns of predicted conserved miRNAs were analyzed by deep sequencing using small RNA sequences of flower buds, leaves, and lateral roots. We have found that many of the identified miRNAs showed tissue specific expressions. Using the insilico method, 346 potential targets were identified for the predicted 69 conserved miRNAs by searching the ginseng EST database, and the predicted targets were mainly involved in secondary metabolic processes, responses to biotic and abiotic stress, and transcription regulator activities, as well as a variety of other metabolic processes.

• 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.

• Korean Journal of Agricultural Science
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• v.45 no.3
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• pp.385-400
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• 2018

Marker-assisted backcrossing (MABC) is useful for selecting offspring with a highly recovered genetic background for a recurrent parent at early generation unlike rice and other field crops. Molecular marker sets applicable to practical MABC are scarce in vegetable crops including tomatoes. In this study, we used the National Center for Biotechnology Information- short read archive (NCBI-SRA) database that provided the whole genome sequences of 234 tomato accessions and selected 27,680 tag-single nucleotide polymorphisms (tag-SNPs) that can identify haplotypes in the tomato genome. From this SNP dataset, a total of 143 tag-SNPs that have a high polymorphism information content (PIC) value (> 0.3) and are physically evenly distributed on each chromosome were selected as a MABC marker set. This marker set was tested for its polymorphism in each pairwise cross combination constructed with 124 of the 234 tomato accessions, and a relatively high number of SNP markers polymorphic for the cross combination was observed. The reliability of the MABC SNP set was assessed by converting 18 SNPs into Luna probe-based high-resolution melting (HRM) markers and genotyping nine tomato accessions. The results show that the SNP information and HRM marker genotype matched in 98.6% of the experiment data points, indicating that our sequence analysis pipeline for SNP mining worked successfully. The tag-SNP set for the MABC developed in this study can be useful for not only a practical backcrossing program but also for cultivar identification and F1 seed purity test in tomatoes.

• Journal of Animal Science and Technology
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• v.57 no.12
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• pp.47.1-47.10
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• 2015

Background: Knowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data. Results: A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the $r^2$ criterion were computed by grouping all syntenic SNP pairwises for intermarker distances from 0 Kb up to 1 Mb using three distance sets. Average $r^2$ above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations. Conclusions: A wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.

• Journal of Microbiology and Biotechnology
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• v.27 no.8
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• pp.1419-1427
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• 2017

As probiotics play an important role in maintaining a healthy gut flora environment through antitoxin activity and inhibition of pathogen colonization, they have been of interest to the medical research community for quite some time now. Probiotic bacteria such as Lactobacillus plantarum, which can be found in fermented food, are of particular interest given their easy accessibility. We performed whole-genome sequencing and genomic analysis on a GB-LP1 strain of L. plantarum isolated from Korean traditional fermented food; this strain is well known for its functions in immune response, suppression of pathogen growth, and antitoxin effects. The complete genome sequence of GB-LP1 is a single chromosome of 3,040,388 bp with 2,899 predicted open reading frames. Genomic analysis of GB-LP1 revealed two CRISPR regions and genes showing accelerated evolution, which may have antibiotic and antitoxin functions. The aim of the present study was to predict strain specific-genomic characteristics and assess the potential of this new strain as lactic acid bacteria at the genomic level using in silico analysis. These results provide insight into the L. plantarum species as well as confirm the possibility of its utility as a candidate probiotic.