Plant genomics lab.

생물학은 생물현상을 관찰하고 그에 맞는 가설을 세우고 꾸준히 증명해나가는 학문입니다. 생물현상의 관찰값이 많지 않던 과거와는 달리 최근 기술의 발전에 따라 생물 빅 데이터라고 불리울 만큼 많은 데이터를 생산하고 있습니다. 이에 생물현상의 관찰값이 대량화되어 “생물정보”를 다루는 학문이 정착하였는데 그것이 생물 정보학입니다. 특히 저렴한 가격으로 꾸준히 생산되고 있는 생물정보는 Next generation sequencer (NGS) 데이터입니다. Genome,Transcriptome, Epigenome, Interactome 등의 데이터가 과거에 비해 빠른속도로 축적되고 있는데 이를 통합하여 생명현상을 충분히 설명할 수 있는 모델을 만들고자 하는 것이 본 실험실의 주 목적입니다. 이는 생물 유전자원을 쉽게 대표할 수 있는 1. Genome profile 개발 그리고 2. Genome profile 기반의 인공지능 예측 모델을 통한 작물육종 시스템 개발 3, Portable sequencer를 통한 유전체 기반 검역시스템을 개발하여 실용화 하기위해 노력하고 있습니다. 앞으로 생물정보학은 생물학을 수행하기 위해 필수 학문이 될것으로 예상됩니다. 끊임없이 쏟아져 나오는 데이터들은 우리가 이미 알고 있던 가설들을 무너뜨리기도 하고 더욱더 강력한 가설들을 제시할 것 입니다. 또한 생물학이라는 분야에서 이루어낸 성취들을 실생활에 적용하는데 역시 생물정보학은 중요한 역할을 할 것으로 기대합니다. 이러한 생물정보시대에 대비한 잘 훈련된 젊은 연구자들이 미래의 생물학을 이끌어나갈 것이라고 생각합니다.

Hosting DBs

DB name Description Link
Human geneID annotator Human geneID (only ensembl ID) will be annotated and can be downloaded as CSV
W.australiana DB W.australiana genome and transcriptome DB
GONET GO enrichment analysis and its visualization by d3.js
KeggNet Viewer Network visualization for Kegg Classification
TandemDB.lemna TandemDB.lemna is a web app to determine whether query genes are enriched by tandem duplicates or not
soy_vcf2genome Soy_VCF2Genome is WebApp to identify the nearest cultivar or germplasm for the single VCF file.
SoyPed SoyPed is for visualization of soybean breeding pedigree
riceqtl riceqtl is for listing reported QTL in rice genome.
sugarcane_orf_finder Sugarcane_orf_finder is designed to search the nearest homolog in sugar cane genome and find ORF using transcriptome assembly.
protein2vector Protein2vector is string kernel based nearest protein search algorithm.
WEBWEB.ara Web-based web (network) visualization WEBWEB. WEBWEB.ara shows diverse pre-defined networks for providing insights on the candidate genes from many experiments

Published papers

Genome sequence of Jatropha curcas L., a non‐edible biodiesel plant, provides a resource to improve seed‐related traits
None
Jatropha curcas (physic nut), a non‐edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up‐regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.
Defenses Against Brown Planthopper Through Transcriptomic and Metabolic Changes in Rice
June 8, 2019, 5:18 p.m.
Brown planthopper (BPH; Nilaparvata lugens Stål) is one of the most serious insect pests, which reduce rice yield remarkably in many rice-growing areas. A few plant growth-promoting rhizobacteria induce systemic resistance against herbivorous insects. Here we show that root drenching of rice seedlings with an endophytic strain Bacillus velezensis YC7010 enhanced defenses against BPH. Based on high-throughput transcriptome analysis, systemic resistance against BPH was induced by B. velezensis YC7010 via salicylic acid (SA)- and jasmonic acid (JA)-dependent pathways. Increased leaf contents of secondary metabolites, tricin and C-glycosyl flavone and cell-wall contents of lignin and cellulose were the key defense mechanisms inducing resistance against BPH during the three-way interaction. This study shows for the first time that chemical changes and strengthening of physical barriers play important roles simultaneously in plant defense against BPH in rice by the endophytic bacteria. This defense was induced by lipopeptides including a novel bacillopeptin X.
Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance
None
Bacterial wilt (BW) is a widespread plant disease that affects a broad range of dicot and monocot hosts and is particularly harmful for solanaceous plants, such as pepper, tomato, and eggplant. The pathogen responsible for BW is the soil-borne bacterium, Ralstonia solanacearum, which can adapt to diverse temperature conditions and is found in climates ranging from tropical to temperate. Resistance to BW has been detected in some pepper plant lines; however, the genomic loci and alleles that mediate this are poorly studied in this species. We resequenced the pepper cultivars YCM344 and Taean, which are parental recombinant inbred lines (RIL) that display differential resistance phenotypes against BW, with YCM344 being highly resistant to infection with this pathogen. We identified novel single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) that are only present in both parental lines, as compared to the reference genome and further determined variations that...
Translational genomics for plant breeding with the genome sequence explosion
None
The use of next‐generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.
Draft genome sequence of adzuki bean, Vigna angularis
None
Adzuki bean (Vigna angularis var. angularis) is a dietary legume crop in East Asia. The presumed progenitor (Vigna angularis var. nipponensis) is widely found in East Asia, suggesting speciation and domestication in these temperate climate regions. Here, we report a draft genome sequence of adzuki bean. The genome assembly covers 75% of the estimated genome and was mapped to 11 pseudo-chromosomes. Gene prediction revealed 26,857 high confidence protein-coding genes evidenced by RNAseq of different tissues. Comparative gene expression analysis with V. radiata showed that the tissue specificity of orthologous genes was highly conserved. Additional re-sequencing of wild adzuki bean, V. angularis var. nipponensis, and V. nepalensis, was performed to analyze the variations between cultivated and wild adzuki bean. The determined divergence time of adzuki bean and the wild species predated archaeology-based domestication time. The present genome assembly will accelerate the genomics-assisted breeding of adzuki bean.
Genome sequence of mungbean and insights into evolution within <i>Vigna</i> species
Nov. 11, 2014, 8:36 a.m.
Mungbean is a fast-growing and warm-season legume crop, cultivated mainly in Asia. Here, the authors sequence the genomes of both wild and domesticated mungbean varieties and, together with detailed transcriptome data, provide insight into mungbean domestication, polyploidization and speciation.
Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection
None
The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment. Here, we developed a web-application, “Soybean-VCF2Genomes”, http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering....
Genome-wide DNA methylation profile in mungbean
None
DNA methylation on cytosine residues is known to affect gene expression and is potentially responsible for the phenotypic variations among different crop cultivars. Here, we present the whole-genome DNA methylation profiles and assess the potential effects of single nucleotide polymorphisms (SNPs) for two mungbean cultivars, Sunhwanogdu (VC1973A) and Kyunggijaerae#5 (V2984). By measuring the DNA methylation levels in leaf tissue with the bisulfite sequencing (BSseq) approach, we show both the frequencies of the various types of DNA methylation and the distribution of weighted gene methylation levels. SNPs that cause nucleotide changes from/to CHH – where C is cytosine and H is any other nucleotide – were found to affect DNA methylation status in VC1973A and V2984. In order to better understand the correlation between gene expression and DNA methylation levels, we surveyed gene expression in leaf tissues of VC1973A and V2984 using RNAseq. Transcript expressions of paralogous genes were controlled by DNA methylation within the VC1973A genome. Moreover, genes that were differentially expressed between the two cultivars showed distinct DNA methylation patterns. Our mungbean genome-wide methylation profiles will be valuable resources for understanding the phenotypic variations between different cultivars, as well as for molecular breeding.
Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean
None
R genes are a key component of genetic interactions between plants and biotrophic bacteria and are known to regulate resistance against bacterial invasion. The most common R proteins contain a nucleotide-binding site and a leucine-rich repeat (NBS-LRR) domain. Some NBS-LRR genes in the soybean genome have also been reported to function in disease resistance. In this study, the number of NBS-LRR genes was found to correlate with the number of disease resistance quantitative trait loci (QTL) that flank these genes in each chromosome. NBS-LRR genes co-localized with disease resistance QTL. The study also addressed the functional redundancy of disease resistance on recently duplicated regions that harbor NBS-LRR genes and NBS-LRR gene expression in the bacterial leaf pustule (BLP)-induced soybean transcriptome. A total of 319 genes were determined to be putative NBS-LRR genes in the soybean genome. The number of NBS-LRR genes on each chromosome was highly correlated with the number of...

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OMICs analysis 학부생
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