A5071028215- Plant Virus Research Studies
- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Plant Gene Expression Analysis
- Genomics and Phylogenetic Studies
- Plant-Microbe Interactions and Immunity
- Plant Disease Resistance and Genetics
- Plant Reproductive Biology
- Plant Pathogenic Bacteria Studies
- Advances in Cucurbitaceae Research
- Plant Pathogens and Fungal Diseases
- Cocoa and Sweet Potato Agronomy
- Plant Pathogens and Resistance
- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- RNA and protein synthesis mechanisms
- Plant tissue culture and regeneration
- Ginseng Biological Effects and Applications
- Legume Nitrogen Fixing Symbiosis
- Plant biochemistry and biosynthesis
- Plant and Fungal Interactions Research
- Food Quality and Safety Studies
- Plant Parasitism and Resistance
- Plant Stress Responses and Tolerance
- Genetics and Plant Breeding
University of Seoul
2020-2024
Seoul National University
2013-2022
Doil Choi and colleagues report the genome sequence of hot pepper, Capsicum annuum, as well resequencing two cultivated peppers a wild species, chinense. Comparative genomic analysis across Solanaceae provides insights into expansion, pungency, ripening disease resistance in peppers. Hot pepper (Capsicum annuum), one oldest domesticated crops Americas, is most widely grown spice crop world. We whole-genome sequencing assembly (Mexican landrace annuum cv. CM334) at 186.6× coverage. also de...
Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable in the expansion nucleotide-binding leucine-rich-repeat proteins (NLRs), disease-resistance gene families, has been unexplored plants.We report two high-quality de novo genomes (Capsicum baccatum C. chinense) an improved reference (C. annuum) for peppers. Dynamic rearrangements involving translocations among chromosomes 3, 5, 9 were detected...
Summary Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil genomic architecture tetraploid P. by de novo assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated diploid species diverged in association global warming Southern Asia, two North American evolved via intercontinental migrations. Two whole duplications (...
Transcription activator-like effector (TALE) proteins of the plant pathogenic bacterial genus Xanthomonas bind to and transcriptionally activate host susceptibility genes, promoting disease. Plant immune systems have taken advantage this mechanism by evolving TALE binding sites upstream resistance (R) genes. For example, pepper Bs3 rice Xa27 genes are hypersensitive reaction R that activated corresponding TALEs. Both a hallmark expression pattern in which their transcripts detectable only...
Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there few studies on QTL mapping of horticultural in pepper (Capsicum spp.) due to the lack high-density molecular maps and sequence information. In this study, an ultra-high-density map 120 recombinant inbred lines (RILs) derived from a cross between C. annuum'Perennial' annuum'Dempsey' were used for traits. Parental RILs resequenced at 18× 1× coverage, respectively. Using sliding window approach, bin...
Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR) receptors are known play critical roles in effector-triggered immunity (ETI) plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes pepper, tomato, potato using fixed criteria. then compared genomic duplication evolution features. identified intact 267, 443, 755 NLR-encoding...
The DNA-binding with one zinc finger proteins (Dofs) are a plant-specific family of transcription factors. Dofs involved in variety biological processes such as phytohormone production, seed development, and environmental adaptation. have been previously identified several plants, but not pepper. We 33 putative Dof genes pepper (CaDofs). To gain an overview the CaDofs, we analyzed phylogenetic relationships, protein motifs, evolutionary history. divided containing 25 into four major groups...
Summary Plants have evolved hundreds of nucleotide‐binding and leucine‐rich domain proteins ( NLR s) as potential intracellular immune receptors, but the evolutionary mechanism leading to ability recognize specific pathogen effectors is elusive. Here, we cloned Pvr4 (a Potyvirus resistance gene in Capsicum annuum ) Tsw Tomato spotted wilt virus chinense via a genome‐based approach using independent segregating populations. The genes both encode typical s are located at same locus on pepper...
MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nt in length which play important roles regulating gene expression plants. Although many miRNA studies have focused on few model plants, miRNAs and their target genes remain largely unknown hot pepper (Capsicum annuum), one the most crops cultivated worldwide. Here, we employed high-throughput sequencing technology to identify extensively from 10 different libraries, including leaf, stem, root, flower, six developmental stage...
Hibiscus syriacus (L.) (rose of Sharon) is one the most widespread garden shrubs in world. We report a draft H. genome comprised 1.75 Gb assembly that covers 92% with only 1.7% (33 Mb) gap sequences. Predicted gene modeling detected 87,603 genes, mostly supported by deep RNA sequencing data. To define family distribution among relatives syriacus, orthologous sets containing 164,660 genes 21,472 clusters were identified OrthoMCL analysis five plant species, including Arabidopsis thaliana,...
Although plant genome sizes are extremely diverse, the mechanism underlying expansion of huge genomes that did not experience whole-genome duplication has been elucidated. The pepper, Capsicum annuum, is an excellent model for studies due to its large size (2700 Mb) and absence whole duplication. As most pepper structure identified as constitutive heterochromatin, we investigated evolution this region in detail. Our findings show heterochromatin was actively expanded 20.0-7.5 million years...
An intraspecific genetic map for watermelon was constructed using an F2 population derived from 'Arka Manik' × 'TS34' and transcript sequence variants quantitative trait loci (QTL) resistance to powdery mildew (PMR), seed size (SS), fruit shape (FS) were analyzed. The consists of 14 linkage groups (LGs) defined by 174 cleaved amplified polymorphic sequences (CAPS), 2 derived-cleaved markers, 20 sequence-characterized regions, 8 expressed tag-simple repeat markers spanning 1,404.3 cM, with a...
Chemical barriers contribute to nonhost resistance, which is defined as the resistance of an entire plant species nonadapted pathogen species. However, molecular basis metabolic defense in remains elusive. Here, we report genetic evidence for essential role phytoalexin capsidiol pepper (Capsicum spp.) potato late blight Phytophthora infestans using transcriptome and genome analyses. Two different genes biosynthesis, 5-epi-aristolochene synthase (EAS) 5-epi-aristolochene-1,3-dihydroxylase...
Abstract Background Among the Solanaceae plants, pepper genome is three times larger than that of tomato. Although gene repertoire and order both species are well conserved, cause genome-size difference not known. To determine causes for expansion euchromatic regions, we compared to Results For sequence-level analysis, generated 35.6 Mb genomic sequences from euchromatin enriched 1,245 BAC clones. The comparative analysis orthologous gene-rich regions between revealed insertion transposons...
Zoysiagrass (Zoysia japonica Steud.) is commonly found in temperate climate regions and widely used for lawns, part, owing to its uniform green color. However, some zoysiagrass cultivars accumulate red purple pigments their spike stolon tissues, thereby decreasing the aesthetic value. Here we analyzed anthocyanin contents of two 'Anyang-jungji' (AJ) 'Greenzoa' (GZ) that produce spikes stolons with colors, respectively, revealed cyanidin petunidin were primarily accumulated pigmented tissues....
Abstract Hot pepper ( Capsicum annuum ) is one of the most consumed vegetable crops in world and useful to human as it has many nutritional medicinal values. Genomic resources are publically available since genomes have been completed massive data such transcriptomes deposited. Nevertheless, global transcriptome profiling needed identify molecular mechanisms related agronomic traits pepper, but limited analyses published. Here, we report comprehensive analysis during fruit ripening pathogen...
Summary Whole‐genome annotation error that omits essential protein‐coding genes hinders further research. We developed Target Gene Family Finder ( TGFam‐Finder ), an alternative tool for the structural of containing target domain(s) interest in plant genomes. took considerably reduced run‐time and improved accuracy compared to conventional tools. Large‐scale re‐annotation 50 genomes identified average 150, 166 86 additional far‐red‐impaired response 1, nucleotide‐binding leucine‐rich‐repeat,...
The AP2/ERF gene family is a superfamily of transcription factors that are important in the response plants to abiotic stress and development. However, comprehensive research genes Solanaceae lacking.Here, we updated annotation genomes eight species, as well Arabidopsis thaliana Oryza sativa. We identified 2,195 genes, which 368 (17%) were newly identified. Based on phylogenetic analyses, observed expansion copy number these especially those belonging specific Ethylene-Responsive Factor...
MicroRNAs (miRNAs) play roles in various biological processes plants including growth, development, and disease resistance. Previous studies revealed that some plant miRNAs produce secondary small interfering RNAs (siRNAs) such as phased, siRNAs (phasiRNAs), they regulate a cascade of gene expression. We performed genome-wide comparative analysis Solanaceous species (pepper, tomato, potato), from an evolutionary perspective. Microsynteny was analysed based on the genomic loci their flanking...
The plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays an important role in epigenetics by regulating expression eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies.We performed genome-wide re-annotation Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice), Capsicum annuum (pepper), Solanum tuberosum (potato), lycopersicum (tomato) better understand the these species....
Abstract Oriental melon ( Cucumis melo L. var. makuwa ) is one of the most important cultivated cucurbits, and grown widely in Northeast Asian countries. With increasing interest its biological properties economic importance, oriental has become an attractive model crop for studying various horticultural traits. A previous genome sequence was constructed from a homozygous double-haploid line. Thus, individual reference genomes are required to perform functional studies further breeding...
Transposable element (TE)-derived genes are increasingly recognized as major sources conferring essential traits in agriculturally important crops but underlying evolutionary mechanisms remain obscure. We updated previous annotations and constructed 18,744 FAR-RED IMPAIRED RESPONSE1 (FAR1) genes, a transcription factor family derived from Mutator-like elements (MULEs), 80 plant species, including 15,546 omitted annotations. In-depth sequence comparison of the gene repertoire revealed that...