• 생명과학회지
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• 제30권3호
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• pp.291-297
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• 2020

본 연구는 차세대 염기서열 분석법(NGS)을 이용하여 방어의 microsatellite 마커를 개발하고, 개발된 마커를 이용하여 방어 집단의 유전적 특성을 분석하기 위해 수행되었다. 차세대 염기서열 분석 장비인 Illumina Hiseq2500를 이용하여 총 28,873,374개의 read들을 얻어 assembly를 수행한 결과, 전체의 약 1.6%에 해당하는 466,359개의 read들이 assembly 되었으며, 이 read들의 총 길이는 7,247,216,874 bp로 확인되었다. 크기가 518 bp 이상이 되는 contig는 30.729개로 나타났으며, 이 중 microsatellite 영역을 포함하는 contig 132개(0.43%)를 1차로 선별하고, PCR 증폭 여부 및 유전자형 분석을 통해 microsatellite 후보 60개를 2차로 선별하였다. 그 중 방어집단의 마커로서 유용한 15개의 microsatellite 마커를 선택하였다. 방어집단을 대상으로 개발된 15개의 microsatellite 마커로 분석한 결과, 관찰된 유효 대립유전자수(N_A)는 평균 18.5(11~30)로 나타났다. 평균 관측치 이형접합도(H_O)와 평균기대치 이형접합도(H_E)는 각각 0.812(0.431~0.972)와 0.896(0.782~0.949)으로 나타났다. 다형성이 관찰된 모든 microsatellite 마커 간의 연관불평형은 나타나지 않았으며, 해산어의 평균 H_E 값인 0.79 이상의 수치를 나타내었다. 따라서 본 연구에서 개발된 15개의 microsatellite 마커는 방어 집단의 유전적 다양성 분석에 유용할 것으로 사료된다.

• 생명과학회지
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• 제30권1호
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• pp.64-69
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• 2020

꿀벌(Apis mellifera)에는 많은 항균성 펩티드가 있습니다. 그러나 아직 많은 종류의 펩티드를 기능을 알려지지 않았다. 따라서, 알려지지 않은 기능성 펩티드의 특성화가 필요하다. 그래서 우리는 새로운 항균성 펩티드(AMP)를 분석 하였다. 우리는 Apis mellifera에서 total RNA를 분리하고 Illumina HiSeq 2500 차세대 시퀀싱(NGS) 기술을 사용하여 15,314 개의 펩티드 서열을 생성하여 새로운 AMP를 선발 하였다. AMP로서 기능을 가지는 AMP를 선발 하기 위해 AMP 서열의 특성 과 특징을 분석을 기초로 하여 알려지지 않은 펩티드 및 알려진 44 개의 펩티드가 확인 되었다. 그 중에서도 AMP5라는 특성화 되지 않은 펩티드를 선발 하였다. AMP5는 표피, 지방체, 독낭에서 발현된다. 항균 활성을 분석하기 위해 Gram-negative bacteria Escherichia coli KACC 10005 및 Bacillus thuringiensis KACC 10168에 대한 항균 활성을 합성한 AMP5 처리하여 시험 하였다. AMP5는 Gram-negative bacteria Escherichia coli에 대한 항균 활성을 나타냈다(MIC₅₀ = 22.04±0.66 μM). 일벌에 Escherichia coli을 주사했을 때 AMP5는 체내에서 항균성 펩티드로 발현이 높아졌다. 이러한 결과는 Escherichia coli에 대한 항균 활성을 나타냄을 확인하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제24권9호
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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.

• 환경생물
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• 제37권3호
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• pp.380-388
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• 2019

본 연구는 전국 임의의 산양삼 재배지를 선정하여 재배지 내의 토양 특성 및 토양세균군집을 분석하고, 토양 이화학적 특성, 토양세균군집 및 산양삼 생육특성 간의 상관관계를 구명하기 위하여 수행되었다. 토양세균군집 분석은 pyrosequencing analysis (Illumina platform)를 이용하였고, 토양세균군집과 생육특성 간의 상관관계는 Spearman's rank correlation을 이용하여 분석하였다. 8개 산양삼 재배지로부터 분리한 토양세균군집은 2개의 군집으로 군집화를 이루는 것을 확인하였다. 모든 토양샘플에서 Proteobacteria와 Alphaproteobacteria가 각각 35.4%, 24.4%로 가장 높은 상대적 빈도수를 보였다. 산양삼의 생육은 토양 pH가 낮고 Acidobacteria의 상대적 빈도수가 높은 토양에서 증가하였으며, Acidobacteriia (class)와 Koribacteraceae (family)의 상대적 빈도수는 산양삼의 생육과 유의적인 정의 상관관계를 보이는 것으로 나타났다. 본 연구 결과는 토양세균군집과 산양삼 생육 간의 상관관계를 구명하는 중요한 자료가 될 것으로 생각되고, 나아가 산양삼 재배 이전에 산양삼의 생육에 유용한 토양세균군집을 확인할 수 있다면 산양삼 재배적지를 선정하는데 도움을 줄 수 있을 것이다. 또한 토양이화학성과 더불어 임상 및 주변식생에 따른 토양세균군집과 산양삼 생육특성에 대한 상관관계 연구를 추가로 수행한다면 보다 명확한 정보를 대한 제공할 수 있을 것으로 사료된다.

• Journal of Ginseng Research
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• 제40권2호
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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.

• 응용통계연구
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• 제29권6호
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• pp.1117-1128
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• 2016

고차원 유전체 자료를 사용하는 유전체 연관 분석에서는 벌점 우도함수 기반의 회귀계수 규제화 방법이 질병 및 표현형질에 영향을 주는 유전자를 발견하는데 많이 이용된다. 특히, 네트워크 기반의 규제화 방법은 유전체 연관성 연구에서의 유전체 경로나 신호 전달 경로와 같은 생물학적 네트워크 정보를 사용할 수 있으므로, Lasso나 Elastic-net과 같은 다른 규제화 방법들과 비교했을 경우 네트워크 기반의 규제화 방법이 보다 더 정확하게 관련 유전자들을 찾아낼 수 있다는 장점을 가지고 있다. 그러나 네트워크 기반의 규제화 방법은 그룹 구조를 갖고 있는 고차원 유전체 자료에는 적용시킬 수 없다는 문제점을 가지고 있다. 실제 SNP 데이터와 DNA 메틸화 데이터처럼 대다수의 고차원 유전체 자료는 그룹 구조를 가지고 있으므로 본 논문에서는 이러한 그룹 구조를 가지고 있는 고차원 유전체 자료를 분석하고자 네트워크 기반의 규제화 방법에 주성분 분석(principal component analysis; PCA)과 부분 최소 자승법(partial least square; PLS)과 같은 차원 축소 방법을 결합시키는 새로운 분석 방법을 제안하고자 한다. 새롭게 제안한 분석 방법은 몇 가지의 모의실험을 통해 변수 선택의 우수성을 입증하였으며, 또한 152명의 정상인들과 123명의 난소암 환자들로 구성된 고차원 DNA 메틸화 자료 분석에도 사용하였다. DNA 메틸화 자료는 대략 20,000여개의 CpG sites가 12,770개의 유전자에 포함되어 있는 그룹 구조를 가지고 있으며 Illumina Innium uman Methylation27 BeadChip으로부터 생성되었다. 분석 결과 우리는 실제로 암에 연관된 몇 가지의 유전자를 발견할 수 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제26권6호
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• pp.772-779
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• 2013

Linkage disequilibrium (LD) plays an important role in genomic selection and mapping quantitative trait loci (QTL). In this study, the pattern of LD and effective population size ($N_e$) were investigated in Chinese beef Simmental cattle. A total of 640 bulls were genotyped with IlluminaBovinSNP50BeadChip and IlluminaBovinHDBeadChip. We estimated LD for each autosomal chromosome at the distance between two random SNPs of <0 to 25 kb, 25 to 50 kb, 50 to 100 kb, 100 to 500 kb, 0.5 to 1 Mb, 1 to 5 Mb and 5 to 10 Mb. The mean values of $r^2$ were 0.30, 0.16 and 0.08, when the separation between SNPs ranged from 0 to 25 kb to 50 to 100 kb and then to 0.5 to 1 Mb, respectively. The LD estimates decreased as the distance increased in SNP pairs, and increased with the increase of minor allelic frequency (MAF) and with the decrease of sample sizes. Estimates of effective population size for Chinese beef Simmental cattle decreased in the past generations and $N_e$ was 73 at five generations ago.

• Asian-Australasian Journal of Animal Sciences
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• 제30권7호
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• pp.957-966
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• 2017

Objective: To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. Methods: The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database. Results: Metagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways. Conclusion: Yaks' age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks' growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.

• Journal of Microbiology and Biotechnology
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• 제28권6호
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• pp.976-986
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• 2018

Knowledge about the gut bacterial communities associated with insects is essential to understand their roles in the physiology of the host. In the present study, the gut bacterial communities of a laboratory-reared insecticide-susceptible (IS), and a field-collected insecticide-resistant (IR) population of a major rice pest, the brown planthopper Nilaparvata lugens, were evaluated. The deep-sequencing analysis of the V3 hypervariable region of the 16S rRNA gene was performed using Illumina and the sequence data were processed using QIIME. The toxicological bioassays showed that compared with the IS population, IR population exhibited 7.9-, 6.7-, 14.8-, and 18.7-fold resistance to acephate, imidacloprid, thiamethoxam, and buprofezin, respectively. The analysis of the alpha diversity indicated a higher bacterial diversity and richness associated with the IR population. The dominant phylum in the IS population was Proteobacteria (99.86%), whereas the IR population consisted of Firmicutes (46.06%), followed by Bacteroidetes (30.8%) and Proteobacteria (15.49%). Morganella, Weissella, and Enterococcus were among the genera shared between the two populations and might form the core bacteria associated with N. lugens. The taxonomic-to-phenotypic mapping revealed the presence of ammonia oxidizers, nitrogen fixers, sulfur oxidizers and reducers, xylan degraders, and aromatic hydrocarbon degraders in the metagenome of N. lugens. Interestingly, the IR population was found to be enriched with bacteria involved in detoxification functions. The results obtained in this study provide a basis for future studies elucidating the roles of the gut bacteria in the insecticide resistance-associated symbiotic relationship and on the design of novel strategies for the management of N. lugens.

• Journal of Microbiology and Biotechnology
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• 제25권8호
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• pp.1195-1204
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• 2015

Increasing evidence suggests that gut microbiota underpin the development of health and longevity. However, our understanding of what influences the composition of this community of the longevous has not been adequately described. Therefore, illumina sequencing analysis was performed on the gut microbiota of centenarians (aged 100-108 years; RC) and younger elderlies (aged 85-99 years; RE) living in Bama County, Guangxi, China and the elderlies (aged 80-92 years; CE) living in Nanning City, Guangxi, China. In addition, their diet was monitored using a semiquantitative dietary questionary (FFQ 23). The results revealed the abundance of Roseburia and Escherichia was significantly greater, whereas that of Lactobacillus, Faecalibacterium, Parabacteroides, Butyricimonas, Coprococcus, Megamonas, Mitsuokella, Sutterella, and Akkermansia was significantly less in centenarians at the genus level. Both clustering analysis and UniFraq distance analysis showed structural segregation with age and diet among the three populations. Using partial least square discriminate analysis and redundancy analysis, we identified 33 and 34 operational taxonomic units (OTUs) as key OTUs that were significantly associated with age and diet, respectively. Age-related OTUs were characterized as Ruminococcaceae, Clostridiaceae, and Lachnospiraceae, and the former two were increased in the centenarians; diet-related OTUs were classified as Bacteroidales, Lachnospiraceae, and Ruminococcaceae. The former two were deceased, whereas the later one was increased, in the high-fiber diet. The age and high-fiber diet were concomitant with changes in the gut microbiota of centenarians, suggesting that age and high-fiber diet can establish a new structurally balanced architecture of gut microbiota that may benefit the health of centenarians.