• Mycobiology
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• 제51권1호
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• pp.49-59
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• 2023

Antrodia cinnamomea, an edible and medicinal fungus with significant economic value and application prospects, is rich in terpenoids, benzenoids, lignans, polysaccharides, and benzoquinone, succinic and maleic derivatives. In this study, the transcriptome of A. cinnamomea cultured on the wood substrates of Cinnamomum glanduliferum (YZM), C. camphora (XZM), and C. kanehirae (NZM) was sequenced using the high-throughput sequencing technology Illumina HiSeq 2000, and the data were assembled by de novo strategy to obtain 78,729 Unigenes with an N50 of 4,463 bp. Compared with public databases, about 11,435, 6,947, and 5,994 Unigenes were annotated to the Non-Redundant (NR), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genome (KEGG), respectively. The comprehensive analysis of the mycelium terpene biosynthesis-related genes in A. cinnamomea revealed that the expression of acetyl-CoA acetyltransferase (AACT), acyl-CoA dehydrogenase (MCAD), 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA), mevalonate pyrophosphate decarboxylase (MVD), and isopentenyl diphosphate isomerase (IDI) was significantly higher on NZM compared to the other two wood substrates. Similarly, the expression of geranylgeranyltransferase (GGT) was significantly higher on YZM compared to NZM and XZM, and the expression of farnesyl transferase (FTase) was significantly higher on XZM. Furthermore, the expressions of 2,3-oxidized squalene cyclase (OCS), squalene synthase (SQS), and squalene epoxidase (SE) were significantly higher on NZM. Overall, this study provides a potential approach to explore the molecular regulation mechanism of terpenoid biosynthesis in A. cinnamomea.

• Journal of Animal Science and Technology
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• 제65권1호
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• pp.175-182
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• 2023

Antibiotics have been used in livestock production for not only treatment but also for increasing the effectiveness of animal feed, aiding animal growth, and preventing infectious diseases at the time when immunity is lowered due to stress. South Korea and the EU are among the countries that have prohibited the use of antibiotics for growth promotion in order to prevent indiscriminate use of antibiotics, as previous studies have shown that it may lead to increase in cases of antibiotic-resistant bacteria. Therefore, this study evaluated the number of antibiotic resistance genes in piglets staging from pre-weaning to weaning. Fecal samples were collected from 8 piglets just prior to weaning (21 d of age) and again one week after weaning (28 d of age). Total DNA was extracted from the 200 mg of feces collected from the 8 piglets. Whole metagenome shotgun sequencing was carried out using the Illumina Hi-Seq 2000 platform and raw sequence data were imported to Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline for microbial functional analysis. The results of this study did not show an increase in antibiotic-resistant bacteria although confirmed an increase in antibiotic-resistant genes as the consequence of changes in diet and environment during the experiment.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.192-192
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• 2022

Sweetpotato is rich in starch, which is converted to sugar during storage due to enzymatic hydrolysis. The sugar content of sweetpotato is a component related to taste and storability. In this study, the sugar content (fructose, glucose, maltose, sucrose and total sugar content) of 94 genotypes was evaluated and the GWAS (Genome-Wide Association Study) was conducted to search for candidate genes for sugar content. The fructose and glucose content were 0.2 ~ 8.8 and 0.2 ~ 9.4 g/100g, respectively. The maltose, sucrose and total sugar content were 0.2 ~ 9.1,3.2 - 30.0 and 7.9 ~ 40.2 g/100g, respectively. The fructose and glucose showed a positive correlation (0.98). The 94 genotypes were genotyped with genotyping-by-sequencing (GBS) and aligned against the reference genome sequences of sweetpotato. The GBS libraries from 94 genotypes were sequenced on an Illumina HiSeqXten system, and 1,339,892 SNPs (Single Nucleotide Polymorphism) were generated. Filtering for < 60% missing rate and > 0.05 minor allele frequency resulted in a total of 44,255 SNPs used in GWAS. The GAPIT (Genome Association and Prediction Integrated Tool) was used to conduct based on the mean of sugar content with a Bonferroni-corrected chromosome-wide significance threshold with a -logio(P) of 5.95. The significant SNPs were obtained with fructose (seven), glucose (six), maltose (four) and sucrose (nine). There were several genes related to sugar content around the significant SNPs such as sugar transport protein 8-like, probable galactose-1 -phosphate uridyltransferase-like and beta-amylase. These results will contribute to understanding of sugar content and conversion in sweetpotato.

• Journal of Ginseng Research
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• 제38권4호
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• pp.278-288
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• 2014

Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results: Assemblies were generated from ~85 million and ~77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases.We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.

• Reproductive and Developmental Biology
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• 제37권4호
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• pp.233-245
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• 2013

Muscle satellite cell (SC) is responsible for postnatal muscle growth, repair, and regeneration. Satellite cell is an important source of multi-potent stem cell process and differentiation into adipogenic, myogenic, and osteoblastogenic. The objective of this study was to identify alter of transcriptome during differentiation in porcine satellite cell and to elevated transcriptome at different stages of postnatal development to gain insight into the differences in differentiated PSC. We used RNA-seq technique to investigate the transcriptomes during differentiation in pig muscle. Sequence reads were obtained from Illumina HiSeq2000. Differentially expressed genes (DEG) were detected by EdgeR. Gene ontology (GO) terms are powerful tool for unification among representation genes or products. In study of GO biological terms, functional annotation clustering involved in cell cycle, apoptosis, extracellular matrix, phosphorylation, proteolysis, and cell signaling in differences stage. Taken together, these results would be contributed to a better understanding of muscle biology and processes underlying differentiation. Our results suggest that the source of DEGs could be better understanding of the mechanism of muscle differentiation and transdifferentiation.

• 한국가금학회지
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• 제41권4호
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• pp.287-296
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• 2014

조류의 난포 성장은 호르몬의 작용에 따라 크기가 달라져 각각의 단계를 이루며 성장하게 된다. 난의 성숙에 관련된 유전자는 난 단백질 생산과 산란률에 밀접한 관련이 있으며, 이를 유전자 발현 측면에서 심도 있는 고찰이 필요가 있다. 본 연구는 NGS를 이용한 RNA-seq 데이터를 이용하여 유전자의 발현량과 유전자 상호 구조에 대한 분석을 실시하여 난의 발달 과정에 필요한 유전자군을 조사하였다. 본 실험에 사용된 개체는 한국 재래계 흑색계통이 사용되었고, 비교조직은 미성숙란과 성숙란의 RNA를 추출하여 유전자의 발현 양상을 살펴봄으로 난의 성숙에 필요한 유전자의 발현 양상을 보고자 하였다. 실험을 위해 Total RNA를 추출하였고, HiSeq 2000 platform을 사용하여 염기서열을 분석하고, Tuxedo Protocol과 DAVID 프로그램을 통해 유전자의 기능과 상호간의 연관관계를 예측하였다. 탐색된 유전자군은 미성숙란과 성숙란 간에 많은 차이를 보이고 있는 유전자군을 탐색한 결과, 315개의 발현이 다르게 나타나는 것으로 보이고 있으며, GO 분석을 통하여 기능면에서 미성숙란과 성숙란에서 확연히 구분되는 유전자 발현 양상을 확인할 수 있었다. 이들 결과를 통하여 향후 난성숙 과정을 이해하고, 계란 품질 향상을 위한 마커 개발을 기여할 수 있을 것으로 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제30권9호
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• pp.1215-1224
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• 2017

Objective: To assess the differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production, and to obtain new transcriptomic data of these egg-producing ducks. Methods: The Illumina HiSeq 2000 system was used for high throughput sequencing of ovarian transcriptomes from Shan Ma ducks at their peak or late stages of egg production. Results: Greater than 93% of the sequencing data had a base quality score (Q score) that was not less than 20 (Q20). From ducks at their peak stage of egg production, 42,782,676 reads were obtained, with 4,307,499,083 bp sequenced. From ducks at their late stage of egg production, 45,316,166 reads were obtained, with 4,562,063,363 bp sequenced. A comparison of the two datasets identified 2,002 differentially expressed genes, with 790 upregulated and 1,212 downregulated. Further analysis showed that 1,645 of the 2,002 differentially expressed genes were annotated in the non-redundant (NR) database, with 646 upregulated and 999 downregulated. Among the differentially expressed genes with annotations in the NR database, 696 genes were functionally annotated in the clusters of orthologous groups of proteins database, involving 25 functional categories. One thousand two hundred four of the differentially expressed genes with annotations in the NR database were functionally annotated in the gene ontology (GO) database, and could be divided into three domains and 56 categories. The three domains were cellular component, molecular function, and biological process. Among the genes identified in the GO database, 451 are involved in development and reproduction. Analysis of the differentially expressed genes with annotations in the NR database against the Kyoto encyclopedia of genes and genomes database revealed that 446 of the genes could be assigned to 175 metabolic pathways, of which the peroxisome proliferator-activated receptor signaling pathway, insulin signaling pathway, fructose and mannose metabolic pathways, gonadotropin releasing hormone signaling pathway and transforming growth factor beta signaling pathway were significantly enriched. Conclusion: The differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production were elucidated, which greatly enriched the ovarian transcriptomic information of egg-producing ducks.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 추계학술대회
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• pp.73-73
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• 2018

Bacterial leaf blight(BLB), caused by X. oryzae pv. oryzae(Xoo), is one of the most destructive diseases of rice due to its high epidemic potential. Understanding BLB resistance at a genetic level is important to further improve the rice breeding that provides one of the best approaches to control BLB disease. In the present investigation, a collection of 192 accessions was used in the genome-wide association study (GWAS) for BLB resistance loci against four Korean races of Xoo that were represented by the prevailing BLB isolates under Xoo differential system. A total of 192 accessions of rice germplasm were selected on the basis of the bioassay using four isolated races of Xoo such as K1, K2, K3 and K3a. The selected accessions was used to prepare 384-plex genotyping by sequencing (GBS) libraries and Illumina HiSeq 2000 paired- end read was used for GBS sequencing. GWAS was conducted using T ASSEL 5.0. The T ASSEL program uses a mixed linear model (MLM). T he results of the bioassay using a selected set of 192 accessions showed that a large number of accessions (93.75%) were resistant to K1 race, while the least number of accessions (34.37%) resisted K3a race. For races K2 and K3, the resistant germplasm proportion remained between 66.67 to 70.83%. T he genotypic data produced SNP matrix for a total of 293,379 SNPs. After imputation the missing data was removed, which exhibited 34,724 SNPs for association analysis. GWAS results showed strong signals of association at a threshold of [-log10(P-value)] more than5 (K1 and K2) and more than4 (K3 and K3a) for nine of the 39 SNPs, which are plausible candidate loci of resistance genes. T hese SNP loci were positioned on rice chromosome 2, 9, and 11 for K1 and K2 races, whereas on chromosome 4, 6, 11, and 12 for K3 and K3a races. The significant loci detected have also been illustrated, NBS-LRR type disease resistance protein, SNARE domain containing protein, Histone deacetylase 19, NADP-dependent oxidoreductase, and other expressed and unknown proteins. Our results provide a better understanding of the distribution of genetic variation of BLB resistance to Korean pathogen races and breeding of resistant rice.

• Molecules and Cells
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• 제38권5호
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• pp.466-473
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• 2015

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

• Asian-Australasian Journal of Animal Sciences
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• 제32권9호
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• pp.1458-1468
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• 2019

Objective: As one of the most important metabolic organs, the liver plays vital roles in modulating the lipid metabolism. This study was to compare miRNA expression profiles of the Large White liver between two different developmental periods and to identify candidate miRNAs for lipid metabolism. Methods: Eight liver samples were collected from White Large of 70-day fetus (P70) and of 70-day piglets (D70) (with 4 biological repeats at each development period) to construct sRNA libraries. Then the eight prepared sRNA libraries were sequenced using Illumina next-generation sequencing technology on HiSeq 2500 platform. Results: As a result, we obtained 346 known and 187 novel miRNAs. Compared with the D70, 55 down- and 61 up-regulated miRNAs were shown to be significantly differentially expressed (DE). Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis indicated that these DE miRNAs were mainly involved in growth, development and diverse metabolic processes. They were predicted to regulate lipid metabolism through adipocytokine signaling pathway, mitogen-activated protein kinase, AMP-activated protein kinase, cyclic adenosine monophosphate, phosphatidylinositol 3 kinase/protein kinase B, and Notch signaling pathway. The four most abundantly expressed miRNAs were miR-122, miR-26a and miR-30a-5p (miR-122 only in P70), which play important roles in lipid metabolism. Integration analysis (details of mRNAs sequencing data were shown in another unpublished paper) revealed that many target genes of the DE miRNAs (miR-181b, miR-145-5p, miR-199a-5p, and miR-98) might be critical regulators in lipid metabolic process, including acyl-CoA synthetase long chain family member 4, ATP-binding casette A4, and stearyl-CoA desaturase. Thus, these miRNAs were the promising candidates for lipid metabolism. Conclusion: Our study provides the main differences in the Large White at miRNA level between two different developmental stages. It supplies a valuable database for the further function and mechanism elucidation of miRNAs in porcine liver development and lipid metabolism.