A5091468537- Mycorrhizal Fungi and Plant Interactions
- Plant Pathogens and Fungal Diseases
- Genomics and Phylogenetic Studies
- Biofuel production and bioconversion
- Nematode management and characterization studies
- Yeasts and Rust Fungi Studies
- Forest Ecology and Biodiversity Studies
- bioluminescence and chemiluminescence research
- Fermentation and Sensory Analysis
- Parasite Biology and Host Interactions
- Fungal and yeast genetics research
- Enzyme Production and Characterization
- Plant and Biological Electrophysiology Studies
- Mycotoxins in Agriculture and Food
- Genetic diversity and population structure
- Fungal Biology and Applications
- Gut microbiota and health
- Slime Mold and Myxomycetes Research
- Polysaccharides and Plant Cell Walls
- Plant Diversity and Evolution
- Genetics, Aging, and Longevity in Model Organisms
- Horticultural and Viticultural Research
- RNA modifications and cancer
- RNA Research and Splicing
- Traditional and Medicinal Uses of Annonaceae
Soochow University
2022-2025
Biodiversity Research Center, Academia Sinica
2013-2023
Academia Sinica
2017-2023
National Chung Hsing University
2009-2017
National Taipei University
2017
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans animals, decimate crop production are a major impediment to socioeconomic development. Here we report broad comparative study 81 genomes parasitic non-parasitic worms. We have identified gene family births hundreds expanded families at key nodes in the phylogeny that relevant parasitism. Examples include modulate host immune responses, enable parasite migration though tissues or...
We present reference-quality genome assembly and annotation for the stout camphor tree (Cinnamomum kanehirae (Laurales, Lauraceae)), first sequenced member of Magnoliidae comprising four orders Magnoliales, Canellales Piperales) over 9,000 species. Phylogenomic analysis 13 representative seed plant genomes indicates that magnoliid eudicot lineages share more recent common ancestry than monocots. Two whole-genome duplication events were inferred within lineage: one before divergence Laurales...
Abstract A ‘sibling’ species of the model organism Caenorhabditis elegans has long been sought for use in comparative analyses that would enable deep evolutionary interpretations biological phenomena. Here, we describe first sibling C . , C. inopinata n. sp., isolated from fig syconia Okinawa, Japan. We investigate morphology, developmental processes and behaviour which differ significantly those The 123-Mb genome was sequenced assembled into six nuclear chromosomes, allowing delineation...
Background & AimsGut dysbiosis plays a role in hepatic encephalopathy (HE), while its relationship at the acute episode of overt HE (AHE), disease progression and clinical outcomes remains unclear. We aimed to identify AHE-specific microbiome association patients' outcomes.MethodsWe profiled fecal changes for cohort 62 patients with cirrhosis AHE i) before treatment, ii) 2-3 days after medication iii) months recovery, three control cohorts healthy individuals, compensated or decompensated...
The ecology and genetic diversity of the model yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part this yeast's geographic birthplace, where most divergent natural lineage was discovered. Here, we extensively sampled broadleaf forests across continental island to probe ancestral species’ diversity. We found that S. distributed ubiquitously at low abundance in forests. Whole-genome sequencing 121 isolates revealed nine distinct...
Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) Smartseq2 to amplify nanograms of genomic DNA mRNA, respectively, individual Caenorhabditis elegans. Although reduced coverage was observed repetitive regions, produced assemblies covering 98% reference using long-read sequences generated with...
Neocallimastix patriciarum is one of the common anaerobic fungi in digestive tracts ruminants that can actively digest cellulosic materials, and its cellulases have great potential for hydrolyzing feedstocks. Due to difficulty culture lack a genome database, it not easy gain global understanding glycosyl hydrolases (GHs) produced by this fungus.We developed an efficient platform uses combination transcriptomic proteomic approaches N. accelerate gene identification, enzyme classification...
Abstract Background Cellulose, which is the most abundant renewable biomass on earth, a potential bio-resource of alternative energy. The hydrolysis plant polysaccharides catalyzed by microbial cellulases, including endo-β-1,4-glucanases, cellobiohydrolases, cellodextrinases, and β-glucosidases. Converting cellobiose β-glucosidases key factor for reducing inhibition enhancing efficiency cellulolytic enzymes cellulosic ethanol production. Results In this study, cDNA encoding β-glucosidase was...
Significance We present the genomes of five new bonnet mushroom Mycena species, formerly last fungal bioluminescent lineage lacking reference genomes. These genome-scale datasets allowed us to construct an evolutionary model pinpointing all possible changes in luciferase cluster across fungi and additional genes involved bioluminescence. show that clusters were differentially lost different lineages particular a substantial loss was observed mycenoid lineage. This can be attributed genome...
Penaeus monodon nudivirus (PmNV) is the causative agent of spherical baculovirosis in shrimp (Penaeus monodon). This disease causes significant mortalities at larval stage and early postlarval (PL) may suppress growth reduce survival production aquaculture. The nomenclature classification status PmNV has been changed several times due to morphological observation phylogenetic analysis its partial genome sequence. In this study, we therefore completed sequence constructed trees clarify PmNV's...
Abstract Background To achieve an economical cellulosic ethanol production, a host that can do both saccharification and fermentation is desirable. However, to engineer non-cellulolytic yeast be such requires synthetic biology techniques transform multiple enzyme genes into its genome. Results A technique, named Promoter-based Gene Assembly Simultaneous Overexpression (PGASO), employs overlapping oligonucleotides for recombinatorial assembly of gene cassettes with individual promoters, was...
Abstract The core of the Vibrio Harveyi clade contains V. harveyi, campbellii, owensii, jasicida , and rotiferianus . They are well recognized aquatic animal pathogens, but misclassification has been common due to similarities in their rDNA sequences phenotypes. To better understand evolutionary relationships functional features, we sequenced a shrimp pathogen strain harveyi 1114GL, reclassified it as campbellii compared this 47 other genomes Harveryi clade. A phylogeny based on 1,775 genes...
The order Hymenochaetales of white rot fungi contain some the most aggressive wood decayers causing tree deaths around world. Despite their ecological importance and impact diseases they cause, little is known about evolution transmission patterns these pathogens. Here, we sequenced undertook comparative genomic analyses genomes using brown root fungus Phellinus noxius, wood-decomposing lamaensis, laminated sulphurascens trunk pathogen Porodaedalea pini. Many gene families lignin-degrading...
Bioluminescence is the emission of light by a luciferin/luciferase chemical reaction within living organisms. There are 40 bioluminescent systems known across tree life, but only handful characterized. While most research has been conducted on bacterial and firefly systems, other organisms, like fungi, use different molecule pairings biochemistries, which can be exploited for various applications. This review covers current understanding fungal bioluminescence diversity, evolution, We...
As a strong fermentator, Saccharomyces cerevisiae has the potential to be an excellent host for ethanol production by consolidated bioprocessing. For this purpose, it is necessary transform cellulose genes into yeast genome because contains no genes. However, heterologous protein expression in S. often suffers from hyper-glycosylation and/or poor secretion. Thus, there need genetically engineer reduce its glycosylation strength and increase secretion ability.Saccharomyces gene-knockout...
Abstract Kluyveromyces marxianus , a probiotic yeast, is important in industrial applications because it has broad substrate spectrum, rapid growth rate and high thermotolerance. To date, however, there been little effort its genetic engineering by the CRISPR/Cas9 system. Therefore, we aimed at establishing system K. creating stable haploid strains, which will make genome simpler. First, predicted genome-wide target sites of that have conserved among eight sequenced genomes strains. Second,...
Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. also species complex with strains exhibiting varying pathogenicity to plants. We present genome and annotations six species, four which belonged complex. Most genomes have size 44.7-47.4 Mb are among smallest clade IV, exception fujianensis, has 143.8 one largest. Phylogenomic analysis successfully delimited into oryzae pseudobesseyi revealed...
Abstract Background The variation in fungal community composition within a single habitat space has been extensively studied forest ecosystems. However, the spatial and temporal distribution of fungi across contiguous habitats, particularly at local scale tropical regions, remains underexplored. In this study, we examined multiple habitats proximal to each other over two seasons seven Fagaceae species Taiwanese broadleaf forests. We tested how influence assembly. Results Using metabarcoding...
Abstract Leaves of the carnivorous sundew plants ( Drosera spp.) secrete mucilage that hosts microorganisms, but whether this microbiota contributes to prey digestion is unclear. We identified acidophilic fungus Acrodontium crateriforme as dominant species in microbial communities, thriving multiple across global range. The grows and sporulates on glands its preferred acidic environment, presence traps increased process. A. has a reduced genome similar other symbiotic fungi. During –...
From mid-December to late January, schools of mature gray mullet (Mugil cephalus) migrate southward along the coastal waters China Taiwan for spawning. It has been proposed that there is no genetic differentiation in Taiwan. To test this hypothesis, complete cytochrome b (cyt b) DNA sequences 98 individuals mullet, two Liza macrolepis, and three L. affinis were amplified by polymerase chain reaction sequenced. Phylogenetic trees reconstructed with Bayesian, maximum likelihood, parsimony,...
Enzymatic conversion of lignocellulosic biomass into soluble sugars is a major bottleneck in the plant utilization. Several anaerobic organisms cope these issues via multiple-enzyme complex system so called 'cellulosome'. Hence, we proposed "biomimic operon" concept for making an artificial cellulosome which can be used as promising tool expression cellulosomal enzymes Bacillus subtilis. According to proteomic analysis Clostridium thermocellum ATCC27405 induced by Avicel or cellobiose,...
Comparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern rearrangement between and within major phyla owing to horizontal gene transfer recombination. The role recombination was exemplified at finer evolutionary time scale in basidiomycetes group fungi as they display diversity DNA inheritance patterns. Here, we assembled mitogenomes six species from the Hymenochaetales order examined 59 2 genetic lineages Phellinus noxius. Gene is largely...