A5101735658- Genomics and Phylogenetic Studies
- Plant Molecular Biology Research
- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- GABA and Rice Research
- Silk-based biomaterials and applications
- Animal Genetics and Reproduction
- Photosynthetic Processes and Mechanisms
- SARS-CoV-2 and COVID-19 Research
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Chromatin Dynamics
- Plant Genetic and Mutation Studies
- Evolution and Genetic Dynamics
- Skin and Cellular Biology Research
- RNA Research and Splicing
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- Rice Cultivation and Yield Improvement
- Plant and Fungal Interactions Research
- RNA and protein synthesis mechanisms
- Aquaculture disease management and microbiota
- Plant Reproductive Biology
University of Chicago
2015-2024
Biodiversity Research Center, Academia Sinica
2015-2024
National Chung Hsing University
2013-2023
Academia Sinica
2011-2023
National Tsing Hua University
2014-2023
University of Southern California
2023
Southern California University for Professional Studies
2023
National Taipei University
2018-2023
Foundation for Advancement of International Science
2023
Shenzhen University
2023
Significance A tumor comprising many cells can be compared to a natural population with individuals. The amount of genetic diversity reflects how it has evolved and influence its future evolution. We evaluated single by sequencing or genotyping nearly 300 regions from the tumor. When data were analyzed modern theory, we estimated more than 100 million coding region mutations in this unexceptional extreme implies evolution under non-Darwinian mode. In contrast, prevailing view Darwinian...
Abstract To study the regulatory and functional differentiation between mesophyll (M) bundle sheath (BS) cells of maize (Zea mays), we isolated large quantities highly homogeneous M BS from newly matured second leaves for transcriptome profiling by RNA sequencing. A total 52,421 annotated genes with at least one read were found in two transcriptomes. Defining a gene more than per kilobase million mapped reads as expressed, identified 18,482 expressed genes; 14,972 cells, including 53...
Histone modifications regulate gene expression in eukaryotes, but their effects on transcriptomes of a multicellular organism and transcriptomic divergence between species are poorly understood. Here we present the first nucleotide-resolution maps histone acetylation, methylation, core Arabidopsis thaliana comprehensive analysis these all other available with data A. thaliana, arenosa , allotetraploids. H3K9 acetylation (H3K9ac) H3K4 trimethylation (H3K4me3) correlated, distribution patterns...
Abstract Binding of a transcription factor (TF) to its DNA binding sites (TFBSs) is critical step initiate the target genes. It therefore interesting know where TFBSs gene are likely locate in promoter region. Here we studied positional distribution Arabidopsis thaliana , for which many known now available. We developed method identify locations sequences genes A. . found that nearly bell-shaped with peak at 50 base pairs (bp) upstream start site (TSS) and 86% region from −1,000 bp +200...
Oral squamous cell carcinoma (OSCC), an epithelial malignancy affecting a variety of subsites in the oral cavity, is prevalent Asia.The survival rate OSCC patients has not improved over past decades due to its heterogeneous etiology, genetic aberrations, and treatment outcomes.Improvement therapeutic strategies tailored options unmet need.To unveil mutational spectrum, whole-exome sequencing 120 from male individuals Taiwan was conducted.Analyzing contributions five signatures extracted...
Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators and their regulatory networks. However, such data 3D (gene expression, time, condition), there is currently no method that can deal with full complexity. Here, we developed avoids time-point alignment normalization between conditions. We applied it to analyze time-series developing maize leaves light-dark cycles total darkness eight time-ordered gene coexpression...
Thermotolerance is a polygenic trait that contributes to cell survival and growth under unusually high temperatures. Although some genes associated with high-temperature (Htg+) have been identified, how cells accumulate mutations achieve prolonged thermotolerance still mysterious. Here, we conducted experimental evolution of Saccharomyces cerevisiae laboratory strain stepwise temperature increases for it grow at 42 °C. Whole genome resequencing 14 evolved strains the parental revealed total...
Abstract We studied the evolution of opsin genes in 59 ray-finned fish genomes. identified and adjacent (syntenies) each genome. Then we inferred changes gene copy number ( N ), syntenies, tuning sites along phylogenetic branch during evolution. The Exorh (rod opsin) has been retained 56 Rh1, intronless rod gene, first emerged ancestral Actinopterygii, increased to 2 by teleost-specific whole genome duplication, but then decreased 1 ancestor Neoteleostei fishes. For cone genes,...
Tetep is a rice cultivar known for broad-spectrum resistance to blast, devastating fungal disease. The molecular basis its still poorly understood. Is it because has many more NLR genes than other cultivars? Or does possess multiple major that can individually confer blast? Moreover, are there interacting pairs in the genome? We sequenced genome, obtained high-quality assembly, and annotated 455 nucleotide-binding site leucine-rich repeat (NLR) genes. cloned tested 219 as transgenes 2...
Gene expression evolution can be caused by changes in cis- or trans-regulatory elements both. As cis and trans regulation operate through different molecular mechanisms, mutations may show inheritance patterns subjected to selective constraints. To investigate these issues, we obtained analyzed gene data from two Saccharomyces cerevisiae strains their hybrid, using high-throughput sequencing. Our indicate that compared with other types of genes, those antagonistic cis–trans interactions are...
Feathers have complex forms and are an excellent model to study the development evolution of morphologies. Existing chicken feather mutants especially useful for identifying genetic determinants formation. This focused on gene F, underlying frizzle trait that has a characteristic curled rachis barbs in domestic chickens. Our developmental biology studies identified defects medulla formation, physical revealed curls stepwise manner. The is transmitted autosomal incomplete dominant mode. A...
Cells govern biological functions through complex networks. Perturbations to networks may drive cells new phenotypic states, for example, tumorigenesis. Identifying how genetic lesions perturb molecular is a fundamental challenge. This study used large-scale human interactome data systematically explore the relationship among network topology, somatic mutation, evolutionary rate, and origin of cancer genes. We found unique centrality proteins, which largely independent gene essentiality....
Antrodia cinnamomea, a polyporus mushroom of Taiwan, has long been used as remedy for cancer, hypertension, and hangover, with an annual market over $100 million (US) in Taiwan. We obtained 32.15-Mb genome draft containing 9,254 genes. Genome ontology enrichment pathway analyses shed light on sexual development the biosynthesis sesquiterpenoids, triterpenoids, ergostanes, antroquinonol, antrocamphin. identified genes differentially expressed between mycelium fruiting body 242 proteins...
Our anatomical analysis revealed that a dry maize seed contains four to five embryonic leaves at different developmental stages. Rudimentary kranz structure (KS) is apparent in the first leaf with substantial density, but its density decreases toward younger leaves. Upon imbibition, expansion occurs rapidly new KSs initiated from palisade-like ground meristem cells middle of leaf. In parallel analysis, we obtained time course transcriptomes for and imbibed seeds every 6 h up hour 72. Over...
Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous changes in physiology, morphology, and behavior have been artificially selected. Genomic study is required to genome-wide patterns DNA variation dissecting traits. We sequenced genomes Silkie Taiwanese native chicken L2 at ∼23- 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto reference genome (including 5.1% Ns) 92.32% two breeds....
Significance Avian skin appendages include feathers, scales, claws, and beaks. They are mainly composed of α-keratins, found in all vertebrates, β-keratins, only birds reptiles. Scientists have wondered how keratins interwoven to form different appendages. By studying keratin gene expression patterns chicken appendages, we α- β-keratin interactions crucial for appendage morphogenesis. Mutations either or β-keratins can disrupt cause structural defects. Thus, combinations contribute the...
Abstract Background Many microorganisms possess enzymes that can efficiently degrade lignocellulosic materials, but do not have the capability to produce a large amount of ethanol. Thus, attempts been made transform such into fermentative microbes serve as hosts for ethanol production. However, an efficient host consolidated bioprocess (CBP) remains be found. For this purpose, synthetic biology technique multiple genes genome is instrumental. Moreover, strategy select cellulases interact...
Cancer development and progression result from somatic evolution by an accumulation of genomic alterations. The effects those alterations on the fitness cells lead to evolutionary adaptations such as increased cell proliferation, angiogenesis, altered anticancer drug responses. However, there are few general mathematical models quantitatively examine how perturbations a single gene shape subsequent cancer genome. In this study, we proposed gravity model study genomes incorporating...
Significance Maize is a major crop and model plant for studying C4 leaf development. However, its regulatory network of development poorly understood. We used transcriptomes developing leaves to study gene-expression dynamics coexpression reveal functional transition during maize More significantly, we developed methods predict transcription factor-binding sites (TFBSs) their cognate factors (TFs) or use the known Arabidopsis TF–TFBS pairs pairs. In total, predicted 1,340 novel TFBSs 253 new...
Feathers are hallmark avian integument appendages, although they were also present on theropods. They composed of flexible corneous materials made α- and β-keratins, but their genomic organization functional roles in feathers have not been well studied. First, we an exhaustive search β-keratin genes the new chicken genome assembly (Galgal4). Then, using transcriptomic analysis, studied gene expression patterns five types feather epidermis. The different types, whereas those α-keratin less...
Significance Finding the genes that control a complex trait is difficult because each gene may have only minor phenotypic effects. Quantitative loci mapping and genome-wide association study techniques been developed for this purpose but are laborious time-consuming. Here we method combining pedigree analysis, whole-genome sequencing, CRISPR-Cas9 technology. By sequencing parents descendants of IR8, Green Revolution “miracle rice,” identified many had retained in by selection high yield....