• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.237-237
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• 2022

Cynodon transvaalensis belongs to the warm-season grasses and is one of the economically and ecologically important crops. Cynodon species with high heterozygosity are difficult to assemble, so genome research has not been actively conducted. In this study, hybrid assembly was performed by sequencing with Illumina and PacBio. As a result of the assembly, the number of scaffolds and the length of N50 were 1,392, 928 kb, respectively. The completeness of the assembly was confirmed by BSUCO at 98.3%. In addition, as a result of estimating the size of the assembled genome by K-mer analysis (k=25), it was approximately ~413 Mb. A total of 37,060 cds sequences were annotated in the assembled genome, and their functions were identified through blast. After that, we try to complete the assembled genome into a pseudochromosome-level genome through Hi-C technology. These results will not only help to understand the complex genome composition of african bermudagrass, but also provide a resource for genomic and evolutionary studies of grass and other plant species.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.1
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• pp.240-246
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• 2020

This study was conducted to develop specific Single Nucleotide Polymorphism (SNP) markers to identify the genetic characteristics and breed of White Hanwoo (WH) using a molecular biological method. SNP genotyping was performed with an Illumina Bovine HD 777K SNP chip using DNA extracted from 48 Hanwoo and 22 WH. The minor allele frequency (MAF) difference of each SNP was calculated and the statistical significance (P-value) of the MAF difference was calculated through Fisher's Exact test (Genotype). SNPs with 100% difference in the MAF difference were selected based on marker selection criteria. The nine SNP markers with genetic differences were selected. The selected markers have different alleles as being Hanwoo- and WH- specific. Therefore, based on these results, it can be concluded that the Hanwoo and WH varieties can be clearly distinguished by using these SNPs. So, the patent of the WH breed identification markers was registered. WH is a breed that shows the characteristics of a Korean native species that is separate from the native Hanwoo. It is expected that genetic characteristics research on the WH can be used to identify the breed and as a knowledge base for enhancing the value of breeding stock.

• Journal of The Korean Society of Grassland and Forage Science
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• v.39 no.4
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• pp.227-234
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• 2019

This study was performed to investigate the effect of heat-stressed environment on rumen microbial diversity in Holstein cows. Rectal temperature and respiration rate were measured and rumen fluid was collected under normal environment (NE; Temperature humidity index (THI)=64.6) and heat-stressed environment (HE; THI=87.2) from 10 Holstein cows (60±17.7 months, 717±64.4 kg) fed on the basis of dairy feeding management in National Institute of Animal Science. The rumen bacteria diversity was analyzed by using the Illumina HiSeq^TM 4000 platform. The rectal temperature and respiratory rate were increased by 1.5℃ and 53 breaths/min in HE compared to that in NE, respectively. In this study, HE exposure induced significant changes of ruminal microbe. At phylum level, Fibrobacteres were increased in HE. At genus level, Ruminococcaceae bacterium P7 and YAD3003, Butyrivibrio sp. AE2032, Erysipelotrichaceae bacterium NK3D112, Bifidobacterium pseudolongum, Lachnospiraceae bacterium FE2018, XBB2008, and AC2029, Eubacterium celulosolvens, Clostridium hathewayi, and Butyrivibrio hungatei were decreased in HE, while Choristoneura murinana nucleopolyhedrovirus, Calothrix parasitica, Nostoc sp. KVJ20, Anabaena sp. ATCC 33047, Fibrobacter sp. UWB13 and sp. UWB5, Lachnospiraceae bacterium G41, and Xanthomonas arboricola were increased in HE. In conclusion, HE might have an effect to change the rumen microbial community in Holstein cows.

• Korean Journal of Environmental Agriculture
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• v.39 no.1
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• pp.1-9
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• 2020

BACKGROUND: The aim of this study was to investigate the soil chemical properties and soil bacterial community of the cropping system for Cnidium officinale Makino. METHODS AND RESULTS: The bacterial community was analyzed for the relative abundance and principal coordinated analysis (PCoA analysis) by using by Illumina Miseq sequencing. The correlation analysis between soil chemical properties and soil bacterial community were analyzed by Spearman's rank correlation and DISTLM analysis. Soil bacterial community (phylum and class) showed two distinct clusters consisting of cluster 1 (first cropping) and cluster 2 (continuous cropping) from 2 different cultivation methods of Cnidium officinale Makino. PCoA and DISTLM analyses showed that soil pH and Ca significantly affected soil bacterial community in cultivation area of Cnidium officinale Makino. In addition, Spearman's rank correlation showed significant correlation between relative abundance (Acidobacteria and Actinobacteria) and soil factors (soil pH and Ca). CONCLUSION: The results of this study were considered to be important for determining the correlation between soil properties and soil bacterial community of the cropping method for Cnidium officinale Makino. Furthermore, the results will be helpful to investigate the cause of continuous cropping injury of the Cnidium officinale Makino by examining the changes of soil properties and soil bacterial communities.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.5
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• pp.738-747
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• 2018

Objective: In a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats' rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen was conducted to elucidate a role of bacterial structure for effective degradation of plant materials. Methods: The metagenomic data had been subjected into Basic Local Alignment Search Tool (BLASTX) algorithm and the National Center for Biotechnology Information non-redundant sequence database. Here the BLASTX hits were further processed by the Metagenome Analyzer program to statistically analyze the abundance of taxa. Results: Microbial community in the rumen is defined by dominance of Bacteroidetes compared to Firmicutes. The ratio of Firmicutes versus Bacteroidetes was 0.36:1. An abundance of Synergistetes was uniquely identified in the goat microbiome may be formed by host genotype. With regard to bacterial lignocellulose degraders, the ratio of lignocellulolytic genes affiliated with Firmicutes compared to the genes linked to Bacteroidetes was 0.11:1, in which the genes encoding putative hemicellulases, carbohydrate esterases, polysaccharide lyases originated from Bacteroidetes were 14 to 20 times higher than from Firmicutes. Firmicutes seem to possess more cellulose hydrolysis capacity showing a Firmicutes/Bacteroidetes ratio of 0.35:1. Analysis of lignocellulolytic potential degraders shows that four species belonged to Bacteroidetes phylum, while two species belonged to Firmicutes phylum harbouring at least 12 different catalytic domains for all lignocellulose pretreatment, cellulose, as well as hemicellulose saccharification. Conclusion: Based on these findings, we speculate that increasing the members of Bacteroidetes to keep a low ratio of Firmicutes versus Bacteroidetes in goat rumen has resulted most likely in an increased lignocellulose digestion.

• Journal of Life Science
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• v.30 no.3
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• pp.291-297
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• 2020

This study was conducted to develop microsatellite markers in Seriola quinqueradiata using next-generation sequencing. A total of 28,873,374 reads were generated on an Illumina Hiseq2500 system, yielding 7,247,216,874 bp sequences. The de novo assembly resulted in 466,359 contigs. A total of 132 contigs (0.43%), including 60 microsatellite loci, were derived from 30,729 contigs longer than 518 bp. A total of 60 primer sets were designed from the 132 microsatellite loci. A total of 15 polymorphic nuclear microsatellite loci were chosen to evaluate population genetic parameters in the parents and offspring. The mean number of effective alleles was 18.5, ranging from 11 to 30. The observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged between 0.431 and 0.972 with an average of 0.812 and from 0.782 to 0.949 with an average of 0.896, respectively. No significant linkage disequilibrium was observed after Bonferroni revision in any loci. The results show that the 15 polymorphic nuclear microsatellite markers can be used to study the population and conservation genetics of S. quinqueradiata in Korea. To ensure the success of artificial seedling production technology, genetic variations between the parent and offspring populations should be monitored, and inbreeding should be controlled.

• Journal of Life Science
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• v.30 no.1
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• pp.64-69
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• 2020

The European honeybee (Apis mellifera L.) has multiple anti-microbial peptides, but many were unknown and demands for their characterization have increased. This study therefore focused on identifying novel anti-microbial peptides (AMPs) from A. mellifera L. To obtain high-throughput transcriptome data of the honeybee, we implemented next-generation sequencing (NGS), isolating novel AMPs from total RNA, and generated 15,314 peptide sequences, including 44 known, using Illumina HiSeq 2500 technology. The uncharacterized peptides were identified based on specific features of possible AMPs predicted in the sequencing analysis. AMP5, one such uncharacterized peptide, was expressed in the epidermis, body fat, and venom gland of the honeybee. We chemically synthesized this peptide and tested its anti-bacterial activity against Gram-negative Escherichia coli (KACC 10005) and Gram-positive Bacillus thuringiensis (KACC 10168) by anti-microbial assay. AMP5 exhibited anti-bacterial activity against E. coli (MIC50=22.04±0.66 μM) but not against B. thuringiensis. When worker bees were injected with E. coli, AMP5 was up-regulated in the body fat. This study therefore identified AMP5 in adult European honeybees and confirmed its anti-bacterial activity against Gram-negative E. coli.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.9
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• pp.1184-1191
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• 2011

We attempted to generate a linkage map using Illumina Porcine 60K SNP Beadchip genotypes of the $F_2$ offspring from Korean native pig (KNP) crossed with Yorkshire (YS) pig, and to identify quantitative trait loci (QTL) using the line-cross model. Among the genotype information of the 62,136 SNPs obtained from the high-density SNP analysis, 45,308 SNPs were used to select informative markers with allelic frequencies >0.7 between the KNP (n = 16) and YS (n = 8) F0 animals. Of the selected SNP markers, a final set of 500 SNPs with polymorphic information contents (PIC) values of >0.300 in the $F_2$ groups (n = 252) was used for detection of thirty meat quality-related QTL on chromosomes at the 5% significance level and 10 QTL at the 1% significance level. The QTL for crude protein were detected on SSC2, SSC3, SSC6, SSC9 and SSC12; for intramuscular fat and marbling on SSC2, SSC8, SSC12, SSC14 and SSC18; meat color measurements on SSC1, SSC3, SSC4, SSC5, SSC6, SSC10, SSC11, SSC12, SSC16 and SSC18; water content related measurements in pork were detected on SSC4, SSC6, SSC7, SSC10, SSC12 and SSC14. Additional QTL of pork quality traits such as texture, tenderness and pH were detected on SSC6, SSC12, SSC13 and SSC16. The most important chromosomal region of superior pork quality in KNP compared to YS was identified on SSC12. Our results demonstrated that a QTL linkage map of the $F_2$ design in the pig breed can be generated with a selected data set of high density SNP genotypes. The QTL regions detected in this study will provide useful information for identifying genetic factors related to better pork quality in KNP.

• Korean Journal of Environmental Biology
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• v.37 no.3
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• pp.380-388
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• 2019

The studies regarding soil bacterial community and correlation analysis of wild-simulated ginseng cultivation area are insufficient. The purpose of this study was to investigate the correlation between soil bacterial community and growth characteristics of wild-simulated ginseng for selection of suitable cultivation area. The bacterial community was investigated by high throughput sequencing technique (Illumina platform). The correlation coefficient between soil bacterial community and growth characteristics were analyzed using Spearman's rank correlation. The soil bacterial community from soil samples of 8 different wild-simulated ginseng cultivated area exhibited two distinct clusters, cluster 1 and cluster 2. The relative abundance of Proteobacteria (35.4%) and Alphaproteobacteria(24.4%) was observed to be highest in all soil samples. The lower soil pH and higher abundance of Acidobacteria resulted in increased growth of wild-simulated ginseng. Additionally, abundance of Acidobacteriia (class) and Koribacteraceae (family) demonstrated significant positive correlation with fresh weight of wild-simulated ginseng. The results of this study clearly state the correlation between growth characteristic and soil bacterial community of wild-simulated ginseng cultivation area, thereby offering effective insight into selection of suitable cultivation area of wild-simulated ginseng.

• Journal of Ginseng Research
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• v.40 no.2
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• pp.127-134
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• 2016

Background: Rhizospheric fungi play an essential role in the plantesoil ecosystem, affecting plant growth and health. In this study, we evaluated the fungal diversity in the rhizosphere soil of 2-yr-old healthy Panax notoginseng cultivated in Wenshan, China. Methods: Culture-independent Illumina MiSeq and culture-dependent techniques, combining molecular and morphological characteristics, were used to analyze the rhizospheric fungal diversity. A diffusion test was used to challenge the phytopathogens of P. notoginseng. Results: A total of 16,130 paired-end reads of the nuclear ribosomal internal transcribed spacer 2 were generated and clustered into 860 operational taxonomic units at 97% sequence similarity. All the operational taxonomic units were assigned to five phyla and 79 genera. Zygomycota (46.2%) and Ascomycota (37.8%) were the dominant taxa; Mortierella and unclassified Mortierellales accounted for a large proportion (44.9%) at genus level. The relative abundance of Fusarium and Phoma sequenceswas high, accounting for 12.9% and 5.5%, respectively. In total,113 fungal isolates were isolated from rhizosphere soil. They were assigned to five classes, eight orders (except for an Incertae sedis), 26 genera, and 43 species based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer. Fusarium was the most isolated genus with six species (24 isolates, 21.2%). The abundance of Phoma was also relatively high (8.0%). Thirteen isolates displayed antimicrobial activity against at least one test fungus. Conclusion: Our results suggest that diverse fungi including potential pathogenic ones exist in the rhizosphere soil of 2-yr-old P. notoginseng and that antagonistic isolates may be useful for biological control of pathogens.