• Genomics & Informatics
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• v.17 no.3
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• pp.32.1-32.6
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• 2019

Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.

• International Journal of Industrial Entomology and Biomaterials
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• v.27 no.2
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• pp.271-276
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• 2013

The Asian honeybee, Apis cerana, is a native honeybee species in Korea which is important in agriculture for pollination and honey production. For better understanding of the physiology of A. cerana, high-throughput Illumina transcriptome sequencing was performed to analyze the gene expression profiles of queen, worker, and larva. A total of 219,799,682 clean reads corresponding to 22.2 Gb of nucleotide sequences was obtained from the whole body total RNA samples. The Apis mellifera reference mRNA sequence database was used to measure the gene expression level with Bowtie2 and eXpress software, and the Illumina short reads were then mapped to 11,459 out of 11,736 A. mellifera reference genes. Total of 9,221 genes with FPKM value greater than 5 of each sample group were subjected to eggNOG with BLASTX for gene ontology analysis. The differential gene expression between queen and worker, and worker and larva were analyzed to screen the overexpressed genes in each sample group. In the queen and worker sample group, total of 1,766 genes were differentially expressed with 887 and 879 genes overexpressed over two folds in queen and worker, respectively. In the worker and larva sample group, total of 1,410 genes were differentially expressed with 1,009 and 401 genes overexpressed over two folds in worker and larva, respectively.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.1
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• pp.28-32
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• 2012

In the present study, we evaluated the informativeness of SNPs genotyped by the Illumina Bovine SNP50K assay in different cattle breeds. To investigate these on a genome-wide scale, we considered 52,678 SNPs spanning the whole autosomal and X chromosomes in cattle. Our study samples consists of six different cattle breeds. Across the breeds approximately 72 and 6% SNPs were found polymorphic and fixed or close to fix in all the breeds, respectively. The variations in the average minor allele frequency (MAF) were significantly different between the breeds studied. The level of average MAF observed in Hanwoo was significantly lower than the other breeds. Hanwoo breed also displayed the lowest number of polymorphic SNPs across all the chromosomes. More importantly, this study indicated that the Bovine SNP50K assay will have reduced power for genome-wide association studies in Hanwoo as compared to other cattle breeds. Overall, the Bovine SNP50K assay described in this study offer a useful genotyping platform for mapping quantitative trait loci (QTLs) in the cattle breeds. The assay data represent a vast and generally untapped resource to assist the investigation of the complex production traits and the development of marker-assisted selection programs.

• Journal of Veterinary Science
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• v.19 no.6
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• pp.798-807
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• 2018

Several studies have reported the effect of absorption of procyanidins and their contribution to the small intestine. However, differences between dietary interventions of procyanidins and interventions via antibiotic feeding in pigs are rarely reported. Following 16S rRNA gene Illumina MiSeq sequencing, we observed that both procyanidin administration for 2 months (procyanidin-1 group) and continuous antibiotic feeding for 1 month followed by procyanidin for 1 month (procyanidin-2 group) increased the number of operational taxonomic units, as well as the Chao 1 and ACE indices, compared to those in pigs undergoing antibiotic administration for 2 months (antibiotic group). The genera Fibrobacter and Spirochaete were more abundant in the antibiotic group than in the procyanidin-1 and procyanidin-2 groups. Principal component analysis revealed clear separations among the three groups. Additionally, using the online Molecular Ecological Network Analyses pipeline, three co-occurrence networks were constructed; Lactobacillus was in a co-occurrence relationship with Trichococcus and Desulfovibrio and a co-exclusion relationship with Bacillus and Spharerochaeta. Furthermore, metabolic function analysis by phylogenetic investigation of communities by reconstruction of unobserved states demonstrated modulation of pathways involved in the metabolism of carbohydrates, amino acids, energy, and nucleotides. These data suggest that procyanidin influences the gut microbiota and the intestinal metabolic function to produce beneficial effects on metabolic homeostasis.

• Microbiology and Biotechnology Letters
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• v.50 no.3
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• pp.404-413
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• 2022

The process of manufacturing craft beer involves a wide variety of spontaneous microorganisms, acting in different stages of the brewing process, that contribute to the distinctive characteristics of each style. The objective of this work was to compare the structure of microbial communities associated with two different craft beer styles (Doppelbock and Märzen lagers), at a late maturation stage, and to identify discriminative, or style-specific taxa. Bacterial and fungal microbial communities were analyzed by Illumina sequencing of 16S rRNA gene of prokaryotes and the ITS 2 spacer of fungi (eukaryotes). Fungal communities in maturating beer were dominated by the yeast Dekkera, and by lactic acid (Lactobacillus and Pediococcus) and acetic acid (Acetobacter) bacteria. The Doppelbock barrels presented more rich and diverse fungal communities. The Märzen barrels were more variable in terms of structure and composition of fungal and bacterial communities, with occurrence of exclusive taxa of fungi (Aspergillus sp.) and bacteria (L. kimchicus). Minority bacterial taxa, differently represented in the microbiome of each barrel, may underlie the variability between barrels and ultimately, the distinctive traits of each style. The composition of the microbial communities indicates that in addition to differences related to upstream stages of the brewing process, the contact with the wood barrels may contribute to the definition of style-specific microbiological traits.

• Mycobiology
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• v.50 no.6
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• pp.448-456
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• 2022

In this study, the roots and rhizosphere soil of Abies koreana and Taxus cuspidata were collected from sites at two different altitudes on Mt. Halla. Ectomycorrhizal fungi (EMF) were identified by Illumina MiSeq sequencing. The proportion of EMF from the roots was 89% in A. koreana and 69% in T. cuspidata. Among EMF in rhizosphere soils, the genus Russula was the most abundant in roots of A. koreana (p < 0.05). The altitude did not affect the biodiversity of EMF communities but influenced fungal community composition. However, the host plants had the most significant effect on EMF communities. The result of the EMF community analysis showed that even if the EMF were isolated from the same altitudes, the EMF communities differed according to the host plant. The community similarity index of EMF in the roots of A. koreana was higher than that of T. cuspidata (p < 0.05). The results show that both altitude and host plants influenced the structure of EMF communities. Conifers inhabiting harsh sub-alpine environments rely strongly on symbiotic relationships with EMF. A. koreana is an endangered species with a higher host specificity of EMF and climate change vulnerability than T. cuspidata. This study provides insights into the EMF communities, which are symbionts of A. koreana, and our critical findings may be used to restore A. koreana.

• Journal of Microbiology and Biotechnology
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• v.27 no.3
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• pp.561-572
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• 2017

The global commercial cultivation of transgenic crops, including glyphosate-tolerant soybean, has increased widely in recent decades with potential impact on the environment. The bulk of previous studies showed different results on the effects of the release of transgenic plants on the soil microbial community, especially rhizosphere bacteria. In this study, comparative analyses of the bacterial communities in the rhizosphere soils and surrounding soils were performed between the glyphosate-tolerant soybean line NZL06-698 (or simply N698), containing a glyphosate-insensitive EPSPS gene, and its control cultivar Mengdou12 (or simply MD12), by a 16S ribosomal RNA gene (16S rDNA) amplicon sequencing-based Illumina MiSeq platform. No statistically significant difference was found in the overall alpha diversity of the rhizosphere bacterial communities, although the species richness and evenness of the bacteria increased in the rhizosphere of N698 compared with that of MD12. Some influence on phylogenetic diversity of the rhizosphere bacterial communities was found between N698 and MD12 by beta diversity analysis based on weighted UniFrac distance. Furthermore, the relative abundances of part rhizosphere bacterial phyla and genera, which included some nitrogen-fixing bacteria, were significantly different between N698 and MD12. Our present results indicate some impact of the glyphosate-tolerant soybean line N698 on the phylogenetic diversity of rhizosphere bacterial communities together with a significant difference in the relative abundances of part rhizosphere bacteria at different classification levels as compared with its control cultivar MD12, when a comparative analysis of surrounding soils between N698 and MD12 was used as a systematic contrast study.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.309-312
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• 2019

Comamonas sp. NLF-7-7 was isolated from biofilter of wastewater treatment plant. The whole-genome sequence of Comamonas sp. NLF-7-7 was analyzed using the PacBio RS II and Illumina HiSeqXten platform. The genome comprises a 3,333,437 bp chromosome with a G + C content of 68.04%, 3,197 total genes, 9 rRNA genes, and 49 tRNA genes. This genome contained pollutants degradation and floc forming genes such as sulfur oxidization pathway (SoxY, SoxZ, SoxA, and SoxB) and floc forming pathway (EpsG, EpsE, EpsF, EpsG, EpsL, and glycosyltransferase), respectively. The Comamonas sp. NLF-7-7 can be used to the purification of wastewater.

• Journal of Marine Life Science
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• v.6 no.1
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• pp.38-46
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• 2021

The blood clam, Tegillarca granosa, is economically important in marine bivalve and is used in fisheries industry among western Pacific Ocean Coasts especially in Korea, China, and Japan. The number of chromosomes in the blood clam is known as 2n=38, but the genome size and genetic information of the genome are not still clear. In order to predict the genomic size of the T. granosa, the in-silico analysis analysed the genomic size using short DNA sequence information obtained using the NGS Illumina HiSeq platform. As a result, the genomic size of T. granosa was estimated to be 770.61 Mb. Subsequently, a draft genome assembly was performed through the MaSuRCA assembler, and a simple sequence repeat (SSR) analysis was done by using the QDD pipeline. 43,944 SSRs were detected from the genome of T. granosa and 69.51% di-nucleotide, 16.68% trinucleotide, 12.96% tetra-nucleotide, 0.82% penta-nucleotide, and 0.03% hexa-nucleotide were consisted. 100 primer sets that could be used for genetic diversity studies were selected. In the future, this study will help identify the genetic diversity of T. granosa and population genetic studies, and further identify the classification of origin between homogenous groups.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.3
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• pp.429-438
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• 2018

Objective: Although the efficacy of Rubus coreanus (RC) byproducts as a feed additive has been recognized, its effects on intestinal microorganisms and the immune system are still unknown. Methods: Six-week-old male rats were treated with 0.5% RC (T1), 1.0% RC (T2), and 1.5% RC (T3) for 4 weeks. Results: We found that treatment with RC byproducts significantly increased the daily gain of body weight and feed intake. Treg-cell differentiation was enhanced in the mesenteric lymph nodes and spleen from the rats fed with RC byproducts. Illumina sequencing showed that bacteria in the phylum Firmicutes decreased and while those in the phylum Bacteroidetes increased in RC-treated groups. Particularly, the pathogenic microorganisms in the family Peptococcaceae decreased, and the non-pathogenic families Lachnospiraceae and S24-7 increased. Quantitative polymerase chain reaction analysis showed that the RC byproducts increased the lactic acid bacteria Bifidobacterium spp., Oscillospira spp., Leuconostoc citreum, and Weissella cibaria in a concentration-dependent manner. Conclusion: RC byproducts may be effective in immunomodulation by affecting intestinal microorganisms.