Tzi-Yuan Wang

Tzi-Yuan Wang
  • PhD
  • Research Specialist at Academia Sinica

About

117
Publications
21,185
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1,534
Citations
Introduction
I am equipped with molecular ecology and evolution, fish genomics and specialized in Nanopore sequencing. my current research topics focus on microbial application and evolution, phylogeography of freshwater fishes, fish genome evolution and interspecific mating behaviour.
Current institution
Academia Sinica
Current position
  • Research Specialist
Additional affiliations
January 2016 - April 2024
Academia Sinica
Position
  • Associate Research Specialist
January 2010 - December 2015
Academia Sinica
Position
  • Assistant Research Specialist

Publications

Publications (117)
Article
Full-text available
We studied the evolution of opsin genes in 59 ray-fnned fsh genomes. We identifed the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intro...
Article
Full-text available
Introduced freshwater fishes considerably influence the ecology and populations of native species. Previous research has revealed that introduced Zacco platypus may hybridize with chubs that are sister but distinct genera. However, we have little knowledge of Z. platypus' mate choice or its impact on Taiwanese chubs. Therefore, this study identifie...
Article
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Background: Over 50 Taiwanese firefly species have been discovered, but scientists lack information regarding most of their genetics, bioluminescent features, and cohabitating phenomena. In this study, we focus on morphological species identification and phylogeny reconstructed by COI barcoding, as well as luminescent characteristics of cohabited...
Article
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Cyprinids (carps, chubs and minnows) possess well-developed hearing and high sensitivity to sound pressure. The sensitive hearing may assist cyprinids with searching for food, territory defense, and mating behavior. Many paired fishes violently shake in sand and gravel while spawning in rivers. However, no study has examined the ecological importan...
Article
The scientific community maintains a high level of pursuit for novel compounds with biological activity. In considering this, we aimed to utilize the predicted data mining approach (PDMA) for the biotransformation of 4-[(2’,4’-Dinitrophenyl)amino]-phenol (DPAP) precursor compound by using Bacillus megaterium tyrosinase (BmTYR) enzyme into novel hyd...
Article
Tyrosinase from Bacillus megaterium (BmTYR) has been demonstrated to hydroxylate loureirin A and B, compounds found in the ethnomeidicine "dragon's blood". Based on the structural similarity, we predicted that BmTYR also hydroxylate 4-hydroxy-2',6'-dimethoxy dihydrochalcone (HDDC) and data mining confirmed the novelty of produced compound, 3,4-dihy...
Article
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Glycosylation is a critical enzymatic modification that involves the attachment of sugar moieties to target compounds, considerably influencing their physicochemical and biological characteristics. This review explored the role of two primary enzyme classes—glycosyltransferases (GTs) and glycoside hydrolases (GHs, glycosidases)—in catalyzing the gl...
Preprint
Glycosylation is a critical enzymatic modification that involves the attachment of sugar moieties to target compounds, considerably influencing their physicochemical and biological characteristics. This review explored the role of two primary enzyme classes—glycosyltransferases (GTs) and glycoside hydrolases (GHs)—in catalyzing the glycosylation of...
Article
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The percomorph fish clade Gobioidei is a suborder that comprises over 2200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their species diversification, we sequenced and annotated the genome of the loach goby, Rhyacichthys aspro, an early-diverging group, and compared it with nine additional Gobioidei spec...
Article
Androgen and estrogen, key sex hormones, were long thought to be exclusively produced by vertebrates. The O 2 -dependent aromatase that converts androgen to estrogen (estrogenesis) has never been identified in any prokaryotes. Here, we report the finding of anaerobic estrogenesis in a Peptococcaceae bacterium ( Phosphitispora sp. strain TUW77) isol...
Preprint
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Chromosome rearrangements significantly influence speciation, but the role of chromosome fission is paradoxical due to its link with unbalanced segregation. The kinetochore reproduction theory suggests that fissions from kinetochore duplication should allow normal segregation, though empirical support remains scarce. In the Opsariichthyini tribe (A...
Article
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Guided by in silico analysis tools and biotransformation technology, new derivatives of natural compounds with heightened bioactivities can be explored and synthesized efficiently. In this study, in silico data mining and molecular docking analysis predicted that glucosides of skullcapflavone II (SKII) were new flavonoid compounds and had higher bi...
Preprint
Androgen and estrogen, key sex hormones, were long thought to be exclusively produced by vertebrates. The O 2 -dependent aromatase that converts androgen to estrogen (estrogenesis) has never been identified in any prokaryotes. Here, we report the discovery of anaerobic estrogenesis in a Peptococcaceae bacterium (strain TUW77) isolated from the gut...
Article
Full-text available
Computational tools can now facilitate screening precursors and selecting suitable biotransformation enzymes for producing new bioactive compounds. This study applied the data-mining approach to screen for candidate precursors of glycosyltransferases to produce new glucosides from 412 commercial natural compounds. Among five candidates, experimenta...
Article
Full-text available
The scientific community actively pursuits novel compounds with biological activities. In this context, our study utilized the predicted data mining approach (PDMA), which can efficiently screen out biotransformable precursor candidates to produce new bioactive compounds. The PDMA was applied to Bacillus megaterium tyrosinase (BmTYR) to form new bi...
Article
Full-text available
The structural modification of natural products using biotransformation is an effective way to produce organic compounds in a regioselective and/or stereoselective manner. O-methylation is a major modification in nature. The predicted data mining approach (PDMA) can efficiently screen out biotransformable precursor candidates to produce new (functi...
Article
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6-Gingerol is a major phenolic compound within ginger (Zingiber officinale), often used in healthcare; however, its lower bioavailability is partly due to its poor solubility. Four bacterial glycosyltransferases (GTs) were tested to glycosylate 6-gingerol into soluble gingerol glucosides. BsUGT489 was a suitable GT to biotransform 6-gingerol into f...
Article
Full-text available
Gingerols are phenolic biomedical compounds found in ginger (Zingiber officinale) whose low aqueous solubility limits their medical application. To improve their solubility and produce novel glucosides, an a-glucosidase (glycoside hydrolase) from Agrobacterium radiobacter DSM 30147 (ArG) was subcloned, expressed, purified, and then confirmed to hav...
Article
Among tetrapod (terrestrial) vertebrates, amphibians remain more closely tied to an amphibious lifestyle than amniotes, and their visual opsin genes may be adapted to this lifestyle. Previous studies have discussed physiological, morphological, and molecular changes in the evolution of amphibian vision. We predicted the locations of the visual opsi...
Preprint
The percomorph fish clade Gobioidei are a suborder that comprises over 2,200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their diversification, we sequenced and annotated the genome of the loach goby, Rhyacichthys aspro, the basal most group, and compared it with nine additional Gobioidei species. Withi...
Article
Full-text available
PCR‐based high‐throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR‐based approaches. Marine drifting animals—zooplankton—play essential ecological roles in the pela...
Article
Full-text available
Developing materials with structural flexibility that permits self‐repair in response to external disturbances remains challenging. Spider silk, which combines an exceptional blend of strength and pliability in nature, serves as an ideal dynamic model for adaptive performance design. In this work, a novel self‐healing material is generated using sp...
Preprint
Developing materials with structural flexibility that permits self-repair in response to external disturbances remains challenging. Spider silk, which combines an exceptional blend of strength and pliability in nature, serves as an ideal dynamic model for adaptive performance design. In this work, a novel self-healing material is generated using sp...
Article
Bacillus megaterium tyrosinase (BmTYR) has been proven an applicable biocatalyst in the ortho-hydroxylation of flavonoids, which usually possess higher antioxidant activity than their precursors. With a predicted data mining approach (PDMA), putative novel bioactive flavonoids from known precursors may be good candidates for biotransformation by Bm...
Article
Full-text available
Abscondita cerata is the most abundant and widely distributed endemic firefly species in Taiwan and is considered a key environmental and ecological indicator organism. In this study, we report the first long-read genome sequencing of Abs. cerata sequenced by Nanopore technology. The draft genome size, 967Mb, was measured through a hybrid approach...
Article
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Due to the paucity of morphological characters and extensive convergent evolution, bivalve classification is a challenging, two-centuries-old problem (Giribet & Wheeler, 2005; Bieler et al., 2014; Lemer et al., 2016; Giribet & Edgecombe, 2020). Consequently, it is not surprising that morphology-based phylogenies conflict with sequence-based phyloge...
Article
Full-text available
Ganoderma sp. contains high amounts of diverse triterpenoids; however, few triterpenoid saponins could be isolated from the medicinal fungus. To produce novel Ganoderma triterpenoid saponins, biotransformation-guided purification (BGP) process was applied to a commercial Ganoderma extract. The commercial Ganoderma extract was partially separated in...
Article
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The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, remain poorly explored due to technological constraints. Using a combinatio...
Article
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The Chinese ricefish (Oryzias sinensis) is a freshwater fish that is regionally endangered in Taiwan. To evaluate its conservation status and further formulate conservation plans for this species in Taiwan, this study analyzed the fish collected from all known localities, including a newly discovered population. The phylogenetic trees based on D-lo...
Preprint
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Marine drifting animals — zooplankton — play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans, and others. Zooplankton are generally considered passive drifting organisms homogeneously distributed throughout waters, where high dispersal is expected. Although em...
Article
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Ha-Soo-Oh is a traditional Chinese medicine prepared from the roots of Polygonum multiflorum Thunb. The herb extract has been widely used in Asian countries as a tonic agent and nutritional supplement for centuries. To identify new bioactive compounds in Chinese herbs, the biotransformation-guided purification (BGP) process was applied to Ha-Soo-Oh...
Article
Full-text available
This study demonstrated the enzymatic hydroxylation of glycitin to 3′-hydroxyglycitin, confirming the structure by mass and nucleic magnetic resonance spectral analyses. The bioactivity assays further revealed that the new compound possessed over 100-fold higher 1,1-diphenyl-2-picrylhydrazine free-radical scavenging activity than the original glyci...
Preprint
Since the first report of SARS-CoV-2 in December 2019, Taiwan has gone through three local outbreaks. Unlike the first two outbreaks, the spatial and temporal origin of the third outbreak (April 20 to November 5, 2021) is still unclear. We assembled and analyzed a data set of more than 6,000 SARS-CoV-2 genomes, including 300 from Taiwan and 5812 re...
Article
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Natural compounds are considered treasures in biotechnology; however, in the past, the process of discovering bioactive compounds is time consuming, and the purification and validation of the biofunctions and biochemistry of compounds isolated from a medicinal herb are tedious tasks. In this study, we developed an economical process called biotrans...
Article
Full-text available
Puerarin (daidzein-8-C-glucoside) is an isoflavone isolated from several leguminous plants of the genus Pueraria. Puerarin possesses several pharmacological properties; however, the poor solubility of puerarin limits its applications. To resolve this poor solubility, Deinococcus geothermalis amylosucrase (DgAS) was used to modify puerarin into more...
Article
Full-text available
High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and inter...
Article
Full-text available
Simple Summary All livings are composed of cells, which contain lipid, proteins, nuclei acids, and saccharides. Saccharides include polysaccharides, oligo saccharides, disaccharides, which are linked by monosaccharides. Monosaccharides such as glucose exist in two forms, named α and β anomer, in solution. In addition, monosaccharides could be linke...
Preprint
Full-text available
High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and inter...
Article
Di-(2-ethylhexyl) phthalate (DEHP) represents the most used phthalate plasticizer with an annual production above the millions of tons worldwide. Due to its inadequate disposal, outstanding chemical stability, and extremely low solubility (3 mg/L), endocrine-disrupting DEHP often accumulates in urban estuarine sediments at concentrations above the...
Article
Full-text available
Simple Summary Nocturnal fireflies are facing various challenges to their survival (e.g., artificial light pollution and extreme climate change). However, there are still no effective diagnostic tools to distinguish firefly species and monitor how their population size and nocturnal behavior change in the wild. Here, we demonstrated that flash inte...
Article
Full-text available
Mangiferin is a natural antioxidant C-glucosidic xanthone originally isolated from the Mangifera indica (mango) plant. Mangiferin exhibits a wide range of pharmaceutical activities. However, mangiferin’s poor solubility limits its applications. To resolve this limitation of mangiferin, enzymatic glycosylation of mangiferin to produce more soluble m...
Article
Full-text available
Vitexin is a C-glucoside flavone that exhibits a wide range of pharmaceutical activities. However, the poor solubility of vitexin limits its applications. To resolve this limitation, two glycoside hydrolases (GHs) and four glycosyltransferases (GTs) were assayed for glycosylation activity toward vitexin. The results showed that BtGT_16345 from the...
Article
Full-text available
8-Hydroxydaidzein (8-OHDe) is a non-natural isoflavone polyphenol isolated from fermented soybean foods. 8-OHDe exhibits a wide range of pharmaceutical activities. However, both the poor solubility and instability of 8-OHDe limit its applications. To resolve the limitations of 8-OHDe, Deinococcus geothermalis amylosucrase (DgAS) has previously been...
Article
Full-text available
The soil bacterium Psychrobacillus sp. strain AK 1817 was isolated from a tropical soil sample collected in Taiwan. Strain AK 1817 biotransforms the ergostane triterpenoid antcin K from the fungus Antrodia cinnamomea . The genome was sequenced using the PacBio RS II platform and consists of one chromosome of 4,096,020 bp, comprising 3,907 protein-c...
Article
Full-text available
Ganoderma lucidum is a medicinal fungus abundant in triterpenoids, its primary bioactive components. Although numerous Ganoderma triterpenoids have already been identified, rare Ganoderma triterpenoid saponins were recently discovered. To create novel Ganoderma saponins, ganoderic acid G (GAG) was selected for biotransformation using four Bacillus...
Article
Full-text available
We sequenced and assembled the complete mitochondrial genome of Abscondita cerata from Nankang, Taipei City, Taiwan. The complete mitogenome of A. cerata is 16,964 bp long, and contains 13 protein-coding, 22 tRNA, and two rDNA genes. Nucleotide compositions of the mitogenome of the A. cerata are A: 43.93%, T: 36.74%, C: 11.05%, and G: 8.28%. The AT...
Article
Full-text available
Ganoderma lucidum is a medicinal fungus whose numerous triterpenoids are its main bioactive constituents. Although hundreds of Ganoderma triterpenoids have been identified, Ganoderma triterpenoid glycosides, also named triterpenoid saponins, have been rarely found. Ganoderic acid A (GAA), a major Ganoderma triterpenoid, was synthetically cascaded t...
Article
Full-text available
Celastrol is a quinone-methide triterpenoid isolated from the root extracts of Tripterygium wilfordii (Thunder god vine). Although celastrol possesses multiple bioactivities, the potent toxicity and rare solubility in water hinder its clinical application. Biotransformation of celastrol using either whole cells or purified enzymes to form less toxi...
Conference Paper
Full-text available
Ganoderic acid A (GAA) is a triterpenoid with identified effective activity, isolated from Ganoderma lucidum. Glycosylation of triterpenoid might improve its anti‐toxin bioactivity and also increase both water solubility and physical‐chemical stability. Glycosylation is carried out by glycosyltransferases (GT, EC 2.4.x.y), a type of enzyme that uti...
Article
Full-text available
Strain GA A07 was identified as an intestinal Bacillus bacterium of zebrafish, which has high efficiency to biotransform the triterpenoid, ganoderic acid A (GAA), into GAA-15-O-β-glucoside. To date, only two known enzymes (BsUGT398 and BsUGT489) of Bacillus subtilis ATCC 6633 strain can biotransform GAA. It is thus worthwhile to identify the respon...
Article
Full-text available
Ribosomal protein (RP) genes encode structural components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. The mecha...
Article
Full-text available
Ganoderic acid A (GAA) is a bioactive triterpenoid isolated from the medicinal fungus Ganoderma lucidum. Our previous study showed that the Bacillus subtilis ATCC (American type culture collection) 6633 strain could biotransform GAA into compound (1), GAA-15-O-β-glucoside, and compound (2). Even though we identified two glycosyltransferases (GT) to...
Preprint
Full-text available
Ribosomal proteins (RPs) genes encode structure components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. How the...
Article
Full-text available
8-Hydroxydaidzein (8-OHDe), an ortho-hydroxylation derivative of soy isoflavone daidzein isolated from some fermented soybean foods, has been demonstrated to possess potent anti-inflammatory activity. However, the isoflavone aglycone is poorly soluble and unstable in alkaline solutions. To improve the aqueous solubility and stability of the functio...
Article
Full-text available
The medicinal fungus Ganoderma lucidum contains many bioactive triterpenoids, ganoderic acid A (GAA) being one of the major ones. The present study explored the microbial biotransformation of GAA, isolating 283 strains of soil actinomycetes and determining their abilities to biotransform GAA with ultra-performance liquid chromatography analysis. On...
Article
Full-text available
Bacillus subtilis ATCC (American type culture collection) 6633 was found to biotransform ganoderic acid A (GAA), which is a major lanostane triterpenoid from the medicinal fungus Ganoderma lucidum. Five glycosyltransferase family 1 (GT1) genes of this bacterium, including two uridine diphosphate-dependent glycosyltransferase (UGT) genes, BsUGT398 a...
Article
Full-text available
Expression of nuptial color is usually energetically costly, and is therefore regarded as an 'honest signal' to reflect mate quality. In order to choose a mate with high quality, both sexes may benefit from the ability to precisely evaluate their mates through optimizing visual systems which is in turn partially regulated by opsin gene modification...
Article
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Functional bacteria that could biotransform triterpenoids may exist in the diverse microflora of fish intestines. Ganoderic acid A (GAA) is a major triterpenoid from the medicinal fungus Ganoderma lucidum. In studying the microbial biotransformation of GAA, dozens of intestinal bacteria were isolated from the excreta of zebrafish. The bacteria’s ab...
Article
Full-text available
8-Hydroxydaidzein (8-OHDe) has been proven to possess some important bioactivities; however, the low aqueous solubility and stability of 8-OHDe limit its pharmaceutical and cosmeceutical applications. The present study focuses on glycosylation of 8-OHDe to improve its drawbacks in solubility and stability. According to the results of phylogenetic a...
Article
Full-text available
Kluyveromyces marxianus, a probiotic yeast, is important in industrial applications because it has a broad substrate spectrum, a rapid growth rate and high thermotolerance. To date, however, there has been little effort in its genetic engineering by the CRISPR/Cas9 system. Therefore, we aimed at establishing the CRISPR/Cas9 system in K. marxianus a...
Article
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The complete mitochondrial genomes of 76 species from 43 genera under Cyprinidae sensu lato were collected to reassess the molecular phylogeny of Opsariichthyinae sensu Liao et al. 2011. The mitogenomes of three species, Candidia barbata, Opsariichthys evolans, and Opsariichthys pachycephalus, were newly sequenced. Phylogenetic trees were reconstru...
Article
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Antcin K is one of the major ergostane triterpenoids from the fruiting bodies of Antrodia cinnamomea, a parasitic fungus that grows only on the inner heartwood wall of the aromatic tree Cinnamomum kanehirai Hay (Lauraceae). To search for strains that have the ability to biotransform antcin K, a total of 4311 strains of soil bacteria were isolated,...
Article
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Feathers, which are mainly composed of α- and β-keratins, are highly diversified, largely owing to duplication and diversification of β-keratin genes during bird evolution. However, little is known about the regulatory changes that contributed to the expressional diversification of β-keratin genes. To address this issue, we studied transcriptomes f...
Article
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3'-Hydroxygenistein can be obtained from the biotransformation of genistein by the engineered Pichia pastoris X-33 strain, which harbors a fusion gene composed of CYP57B3 from Aspergillus oryzae and a cytochrome P450 oxidoreductase gene (sCPR) from Saccharomyces cerevisiae. P. pastoris X-33 mutants with higher 3'-hydroxygenistein production were se...
Article
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Biofuel, the alternative energy, aims to greatly reduce the carbon emissions on earth. Cellulosic ethanol is expected to replace the first generation biofuel made by agriculture crops, such as corn. Lignocelluloses degradation and fermentation efficiencies are the main limitations. Thus, the objective of consolidated bioprocessing is to engineer a...
Article
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We determined the mitochondrial genome (mitogenome) sequence of Nemateleotris decora by using a long polymerase chain reaction (PCR) method and next-generation sequence (NGS) technology. The total length of N. decora mitogenome is 16 502 bp, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control...
Article
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Gene expression evolution occurs through changes in cis- or trans-regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study we investigated the evolution of TFBSs in the promoter regions of d...
Article
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Catadromous fishes migrate between ocean and freshwater during particular phases of their life cycle. The dramatic environmental changes shape their physiological features, e.g. visual sensitivity, olfactory ability, and salinity tolerance. Anguilla marmorata, a catadromous eel, migrates upstream on dark nights, following the lunar cycle. Such beha...
Article
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Background: 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 to transform cellulose genes into the yeast genome because it contains no cellulose genes. However, heterologous protein expression in S. cerevisiae often su...
Article
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Gene expression evolution can be caused by changes in cis- or trans-regulatory elements or both. As cis and trans regulation operate through different molecular mechanisms, cis and trans mutations may show different inheritance patterns and may be subjected to different selective constraints. To investigate these issues, we obtained and analyzed ge...
Article
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Gene regulation change has long been recognized as an important mechanism for phenotypic evolution. We used the evolution of yeast aerobic fermentation as a model to explore how gene regulation has evolved and how this process has contributed to phenotypic evolution and adaptation. Most eukaryotes fully oxidize glucose to CO2 and H2O in mitochondri...
Article
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To study the regulatory and functional differentiation between the mesophyll (M) and bundle sheath (BS) cells of maize (Zea mays), we isolated large quantities of highly homogeneous M and BS cells from newly matured second leaves for transcriptome profiling by RNA sequencing. A total of 52,421 annotated genes with at least one read were found in th...
Article
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Cellulose, which is the most abundant renewable biomass on earth, is a potential bio-resource of alternative energy. The hydrolysis of plant polysaccharides is catalyzed by microbial cellulases, including endo-β-1,4-glucanases, cellobiohydrolases, cellodextrinases, and β-glucosidases. Converting cellobiose by β-glucosidases is the key factor for re...

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