• Asian-Australasian Journal of Animal Sciences
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• 제32권12호
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• pp.1809-1815
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• 2019

Objective: Copy number variations (CNVs) are a major source of genetic diversity complementary to single nucleotide polymorphism (SNP) in animals. The aim of the study was to perform a comprehensive genomic analysis of CNVs based on high density whole-genome SNP markers in Chinese Dongxiang spotted pigs. Methods: We used customized Affymetrix Axiom Pig1.4M array plates containing 1.4 million SNPs and the PennCNV algorithm to identify porcine CNVs on autosomes in Chinese Dongxiang spotted pigs. Then, the next generation sequence data was used to confirm the detected CNVs. Next, functional analysis was performed for gene contents in copy number variation regions (CNVRs). In addition, we compared the identified CNVRs with those reported ones and quantitative trait loci (QTL) in the pig QTL database. Results: We identified 871 putative CNVs belonging to 2,221 CNVRs on 17 autosomes. We further discarded CNVRs that were detected only in one individual, leaving us 166 CNVRs in total. The 166 CNVRs ranged from 2.89 kb to 617.53 kb with a mean value of 93.65 kb and a genome coverage of 15.55 Mb, corresponding to 0.58% of the pig genome. A total of 119 (71.69%) of the identified CNVRs were confirmed by next generation sequence data. Moreover, functional annotation showed that these CNVRs are involved in a variety of molecular functions. More than half (56.63%) of the CNVRs (n = 94) have been reported in previous studies, while 72 CNVRs are reported for the first time. In addition, 162 (97.59%) CNVRs were found to overlap with 2,765 previously reported QTLs affecting 378 phenotypic traits. Conclusion: The findings improve the catalog of pig CNVs and provide insights and novel molecular markers for further genetic analyses of Chinese indigenous pigs.

• Animal Bioscience
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• 제36권1호
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• pp.29-42
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• 2023

Objective: Pigs, an ideal biomedical model for human diseases, suffer from about 50% early embryonic and fetal death, a major cause of fertility loss worldwide. However, identifying the causal variant remains a huge challenge. This study aimed to detect single nucleotide polymorphisms (SNPs) and candidate genes for the number of mummified (NM) piglets using the imputed whole-genome sequence (WGS) and validate the potential candidate genes. Methods: The imputed WGS was introduced from genotyping-by-sequencing (GBS) using a multi-breed reference population. We performed genome-wide association studies (GWAS) for NM piglets at birth from a Landrace pig populatiGWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase on. A total of 300 Landrace pigs were genotyped by GBS. The whole-genome variants were imputed, and 4,252,858 SNPs were obtained. Various molecular experiments were conducted to determine how the genes affected NM in pigs. Results: A strong GWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase 8 (CDK8) gene, which plays a crucial role in embryonic retardation and lethality. Based on the molecular experiments, we found that Y-box binding protein 1 (YBX1) was a crucial transcription factor for CDK8, which mediated the effect of CDK8 in the proliferation of porcine ovarian granulosa cells via transforming growth factor beta/small mother against decapentaplegic signaling pathway, and, as a consequence, affected embryo quality, indicating that this pathway may be contributing to mummified fetal in pigs. Conclusion: A powerful imputation-based association study was performed to identify genes associated with NM in pigs. CDK8 was suggested as a functional gene for the proliferation of porcine ovarian granulosa cells, but further studies are required to determine causative mutations and the effect of loci on NM in pigs.

• 미생물학회지
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• 제44권1호
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• pp.1-9
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• 2008

본 논문은 벼 흰 잎마름병균인 Xanthomonas oryzae pv. oryzae(Xoo)의 병원성 유전자의 분자유전학적 연구현황을 기술하고자 한다. 또한 국내 고유 벼 흰 잎마름병균 KACC10331의 유전체해독 정보를 기반으로 다른 Xanthomonas의 유전체와 비교 분석함으로써, Xoo의 주요 병원성 유전자의 분자구조를 구명하고자 한다. 이를 통해 Xoo 고유 병원성 유전자 탐색 및 기능 해석을 위한 기초자료를 제공하는데 목적이 있다. Xoo 유전체에는 5개 과(family)에 속하는 9 type의 Insertion sequence(IS)가 611 copy로 존재하고 있으며, 주로 병원성 관련 유전자군 주위에 많이 분포하고 있는 것으로 나타났다. 현재까지 연구가 수행된 주요 병원성 관련 유전자인 hypersensitive response and pathogenicity (hrp) 유전자, extracellular polysaccharide (EPS) 유전자, extracellular enzyme 유전자, lipopolysaccharides (LPS) 유전자, 그리고 avilulence 유전자의 분자유전학적 연구현황을 기술하였다.

• 미생물학회지
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• 제55권1호
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• pp.55-57
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• 2019

페놀과 같은 단환성 화합물을 분해하는 미생물인 Runella sp. ABRDSP2 균주는 담수로부터 분리되었다. 원형으로 완성된 하나의 chromosome과 3개의 plasmid로 구성된 유전체는 GC 함량이 44.4%인 총 7,613,819 bp의 크기를 나타내며 6,006개의 유전자를 인코딩하고 있다. ABRDSP2 균주는 monooxygenase, ring-cleaving dioxygenase 및 catechol 1,2-dioxygenase 등의 다수의 방향성 탄화수소를 분해하는 유전자를 함유하고 있다. 이런 전장 유전체는 Runella sp. ABRDSP2 균주가 다양한 생분해능력이 있음을 나타낸다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2020년도 춘계학술대회
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• pp.120-120
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• 2020

Based on the simple sequence repeat (SSR) marker, a Korean wheat core collection were established with 616 wheat accessions. Among them, the SNP genotyping for the entire genome was performed using DNA chip array to clarify the whole genome SNP profiles. Consequently, a total of 35,143 SNPs were found and we re-established a mini-core collection with 247 accessions. Population diversity and phylogenetic analysis revealed genetic diversity and relationships from the mini core set. In addition, genome-wide association study (GWAS) was performed on 19 phenotypic traits; ear type, awn length, culm length, ear length, awn color, seed coat color, culm color, ear color, loading, leaf length, leaf width, seeding stand, cold damage, weight, auricle, plant type, heading stage, maturation period, upright habit, and degree of flag leaf. The GWAS was performed using the fixed and random model circulating probability unification (FarmCPU), which identified 14 to 258 SNP loci related to 19 phenotypic traits. Our study indicates that this Korean wheat mini-core collection is a set of germplasm useful for basic and applied research with the aim of understanding and exploiting the genetic diversity of Korean wheat varieties.

• Journal of Animal Science and Technology
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• 제65권5호
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• pp.1105-1109
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• 2023

Pedi coccus acidilactici CACC 537 was isolated from canine feces and reported to have probiotic properties. We aimed to characterize the potential probiotic properties of this strain by functional genomic analysis. Complete genome sequencing of P. acidilactici CACC 537 was performed using a PacBio RSII and Illumina platform, and contained one circular chromosome (2.0 Mb) with a 42% G + C content. The sequences were annotation revealed 1,897 protein-coding sequences, 15 rRNAs, and 56 tRNAs. It was determined that P. acidilactici CACC 537 genome carries genes known to be involved in the immune system, defense mechanisms, restriction-modification (R-M), and the CRISPR system. CACC 537 was shown to be beneficial in preventing pathogen infection during the fermentation process, help host immunity, and maintain intestinal health. These results provide for a comprehensive understanding of P. acidilactici and the development of industrial probiotic feed additives that can help improve host immunity and intestinal health.

• Asian-Australasian Journal of Animal Sciences
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• 제14권6호
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

• 인삼문화
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• 제3권
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• pp.1-10
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• 2021

인삼은 세계에서 가장 중요한 약용식물 중 하나이다. 본 연구실에서는 국립종자원에 최초로 등록된 인삼 품종 '천풍'을 이용하여 대략 3Gbp의 완성도 높은 유전체 서열과 60,000여개의 유전자를 동정하여 공개하였다. 인삼속 근연종들과의 비교유전체연구를 통해 종의 분화 시기 등을 추정하였고, 이를 통해 고려인삼의 기원과 두 번의 대륙이동을 통한 인삼속의 진화와 분포모델을 확립하였다. 인삼속 18종 중 2종 (고려인삼, 화기삼)은 24쌍의 염색체를 가지는 사배체 식물이며 나머지 16종은 12쌍의 염색체를 가지는 이배체 식물이다. 인삼속과 두릅나무속은 두릅나무과에 속하는 가장 가까운 식물로서 약 8백만년 전에 분화하였다. 인삼속은 약 6백만년 전 베트남 등의 동남아시아에서 러시아와 같은 동북아시아에 이르는 지역의 깊은 숲 속 서늘한 기후와 숲 속의 음지조건에 적응하며 음지식물로 진화했다. 그 기간은 빙하기와 간빙기가 반복되는 시기로 월동 능력이 없는 이배체 인삼종은 대부분 동북아시아 지역에서 멸종하였고 이 과정에 이배체간 종간 교잡종인 이질사배체가 약 2백만년전 만들어졌으며 한반도를 위시한 동북아시아를 중심으로 월동능력을 가진 고려인삼이 태동되었다고 추정된다. 북미에 분포하는 화기삼은 동북아시아 전역에 분포하던 고려인삼이 약 1백만년전에 빙하의 이동과 더불어 대륙간 이주를 통해 새로운 생태 환경에 적응하면서 분화되었다고 판단된다. 반면 대부분의 이배체 인삼종은 고온을 견디지 못하고 월동능력도 없어 동남아시아 지역에서 1,600미터 이상의 고산 지역으로 쫓겨 올라가 연중 서늘한 기후에서 생존하고 있다. 유전체 해독 정보는 인삼의 기원과 진화기작을 추정하는 학문적 성과 뿐 아니라 인삼산업을 보호하고 우수 인삼을 개발하기 위한 실용적인 분자육종 수단에도 매우 효율적으로 활용될 수 있다.

• Genomics & Informatics
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• 제14권4호
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• pp.255-264
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• 2016

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.

• International Journal of Industrial Entomology and Biomaterials
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• 제44권2호
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• pp.65-71
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• 2022

The wild silkmoth Antheraea yamamai Guérin-Méneville, 1861 (Lepidoptera: Saturniidae) is an important producer of silk that is superior to the silk produced by traditional domesticated silkworm. In this study, we sequenced the complete mitochondrial genome (mitogenome) of An. yamamai collected from Jeju Island, which is the southernmost island approximately 100 km offshore southward from the Korean Peninsula. Determining this sequence will be necessary for tracing the biogeographic history of the species and developing molecular markers for identifying the origin of commercial products. Comparison of the sequence divergence among two available and the current mitogenomes revealed a low but substantial number of substitutions, totaling 23 nucleotides in the whole genome. CytB and ND5 showed the highest variability with five and four variations, respectively, suggesting that these regions will be prior regions to target for subsequent biogeographic and diagnosis study. Phylogenetic reconstruction based on all available sequences of Saturniidae showed that An. yamamai is a sister to the congeneric species An. pernyi, corroborating that Antheraea is a highly supported monophyletic group. The tribe Saturniini was clearly non-monophyletic and interrupted by Attacini and Bunaeini.