Browsing by Author "Lin, Yeong-Shin"

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A New Anguilla Species and a Reanalysis of the Phylogeny of Freshwater Eels
(2009-11-01)
Teng, Hui-Yu
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Lin, Yeong-Shin
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Tzeng, Chyng-Shyan
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生物資訊及系統生物研究所
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Institude of Bioinformatics and Systems Biology
Hui-Yu Teng, Yeong-Shin Lin, and Chyng-Shyan Tzeng (2009) A new Anguilla species and a reanalysis of the phylogeny of freshwater eels. Zoological Studies 48(6): 808-822. Evidence of a new species of Anguillid eel, Anguilla huangi sp. nov., was obtained from examining eel specimens collected from the Cagayan River estuary, northern Luzon L, the Philippines. Both glass eels and cultured eels reared in Taiwan for 5 yr were examined. The morphological measurements of A. huangi sp. nov. overlap with those of A. celebesensis Kaup, 1856 and A. interioris Whitley, 1938, so that this new species cannot be distinguished using morphological characteristics alone. We sequenced its complete mitochondrial genome and constructed a phylogeny of all currently recognized freshwater eel species and subspecies based on both molecular and morphological data. Although A. huangi sp. nov. seemed to be morphologically more similar to A. celebesensis, the molecular phylogeny showed a strongly supported clustering of A. huangi sp. nov. and A. interioris. The genetic distance between A. huangi sp. nov. and A. interioris was similar to that between A. anguilla (Linnaeus, 1758) and A. rostrata (Le Sueur, 1817). The distinct molecular phylogeny ensures the specific status of this new freshwater eel. On the other hand, based on the likelihood analyses, the phylogeny of freshwater eels seems to be better represented by polytomies. These polytomies are likely derived from multiple radiation (rapid speciation) events. We further inferred that each radiation event may also have included a large-scale expansion in distribution. The morphological phylogenetic tree generated using the minimum network (MinNet) method was generally consistent with the molecular phylogeny. We also propose a possible evolutionary history for freshwater eels. The Central American Isthmus hypothesis for the dispersal route of the Atlantic eels was supported by various lines of evidence. http://zooIstud.sinica.edu.tw/JournaIs/48.6/808.pdf
A simple method using Pyrosequencing (TM) to identify de novo SNPs in pooled DNA samples
(2011-03-01)
Lin, Yeong-Shin
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Liu, Fu-Guo Robert
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Wang, Tzi-Yuan
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Pan, Cheng-Tsung
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Chang, Wei-Ting
A practical way to reduce the cost of surveying single-nucleotide polymorphism (SNP) in a large number of individuals is to measure the allele frequencies in pooled DNA samples. Pyrosequencing (TM) has been frequently used for this application because signals generated by this approach are proportional to the amount of DNA templates. The Pyrosequencing (TM) pyrogram is determined by the dispensing order of dNTPs, which is usually designed based on the known SNPs to avoid asynchronistic extensions of heterozygous sequences. Therefore, utilizing the pyrogram signals to identify de novo SNPs in DNA pools has never been undertook. Here, in this study we developed an algorithm to address this issue. With the sequence and pyrogram of the wild-type allele known in advance, we could use the pyrogram obtained from the pooled DNA sample to predict the sequence of the unknown mutant allele (de novo SNP) and estimate its allele frequency. Both computational simulation and experimental Pyrosequencing(TM) test results suggested that our method performs well. The web interface of our method is available at http://life.nctu.edu.tw/similar to yslin/PSM/.
Authenticating the use of dried seahorses in the traditional Chinese medicine market in Taiwan using molecular forensics
(2013-09-01)
Chang, Chia-Hao
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Jang-Liaw, Nian-Hong
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Lin, Yeong-Shin
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Fang, Yi-Chiao
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Shao, Kwang-Tsao
Seahorse, which has a unique appearance and exhibits male pregnancy, is a useful component of traditional Chinese medicine (TCM). With the growing demand for TCM, vast amounts of seahorses are harvested from the wild every year and traded internationally. This study investigated 58 dried seahorse samples collected from 23 Chinese herbal medicine stores across Taiwan using molecular forensics. Results showed that eight seahorse species were present in the Taiwan TCM market. Among them, Knysna seahorse (Hippocampus capensis) has an endangered status according to the International Union for Conservation of Nature (IUCN) Red List, while the West African seahorse (Hippocampus algiricus), tiger tail seahorse (Hippocampus comes), thorny seahorse (Hippocampus histrix), great seahorse (Hippocampus kelloggi), yellow seahorse (Hippocampus kuda), hedgehog seahorse (Hippocampus spinosissimus), and three-spot seahorse (Hippocampus trimaculatus) have vulnerable status. Copyright (C) 2013, Food and Drug Administration, Taiwan. Published by Elsevier Taiwan LLC. All rights reserved.
Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes
(2006-09-26)
Lin, Yeong-Shin
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Byrnes, Jake K.
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Hwang, Jenn-Kang
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Li, Wen-Hsiung
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生物科技學系
Many Saccharomyces cerevisiae duplicate genes that were derived from an ancient whole-genome duplication (WGD) unexpectedly show a small synonymous divergence (K-S), a higher sequence similarity to each other than to orthologues in Saccharomyces bayanus, or slow evolution compared with the orthologue in Kluyveromyces waltii, a non-WGD species. This decelerated evolution was attributed to gene conversion between duplicates. Using approximate to 300 WGD gene pairs in four species and their orthologues in non-WGD species, we show that codon-usage bias and protein-sequence conservation are two important causes for decelerated evolution of duplicate genes, whereas gene conversion is effective only in the presence of strong codon-usage bias or protein-sequence conservation. Furthermore, we find that change in mutation pattern or in tDNA copy number changed codon-usage bias and increased the K-S distance between K. waltii and S. cerevisiae. Intriguingly, some proteins showed fast evolution before the radiation of WGD species but little or no sequence divergence between orthologues and paralogues thereafter, indicating that functional conservation after the radiation may also be responsible for decelerated evolution in duplicates.
Complete mitochondrial genome of the longfin mako shark, Isurus paucus (Chondrichthyes, Lamnidae)
(2016-01-02)
Chang, Chia-Hao
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Chiang, Wei-Chuan
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Lin, Yeong-Shin
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Jang-Liaw, Nian-Hong
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Shao, Kwang-Tsao
Here we describe the complete mitochondrial genome sequence of the longfin mako, Isurus paucus, which is a pelagic shark found in temperate and tropical waters. The circle genome (16,704bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.
Complete mitochondrial genome of the megamouth shark Megachasma pelagios (Chondrichthyes, Megachasmidae)
(2014-06-01)
Chang, Chia-Hao
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Shao, Kwang-Tsao
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Lin, Yeong-Shin
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Chiang, Wei-Chuan
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Jang-Liaw, Nian-Hong
Here we describe the complete mitochondrial genome sequence of the megamouth shark, Megachasma pelagios, which is an extremely rare species of deepwater shark. The circle genome (16,694 bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.
Differentiation of visual spectra and nuptial colorations of two Paratanakia himantegus subspecies (Cyprinoidea: Acheilognathidae) in response to the distinct photic conditions of their habitats
(2015-05-01)
Chang, Chia-Hao
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Shao, Yi Ta
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Fu, Wen-Chung
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Anraku, Kazuhiko
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Lin, Yeong-Shin
Background: Vision, an important sensory modality of many animals, exhibits plasticity in that it adapts to environmental conditions to maintain its sensory efficiency. Nuptial coloration is used to attract mates and hence should be tightly coupled to vision. In Taiwan, two closely related bitterlings (Paratanakia himantegus himantegus and Paratanakia himantegus chii) with different male nuptial colorations reside in different habitats. We compared the visual spectral sensitivities of these subspecies with the ambient light spectra of their habitats to determine whether their visual abilities correspond with photic parameters and correlate with nuptial colorations. Results: The electroretinogram ( ERG) results revealed that the relative spectral sensitivity of P. h. himantegus was higher at 670 nm, but lower at 370 nm, than the sensitivity of P. h. chii. Both bitterlings could perceive and reflect UV light, but the UV reflection patterns differed between genders. Furthermore, the relative irradiance intensity of the light spectra in the habitat of P. h. himantegus was higher at long wavelengths (480-700 nm), but lower at short wavelengths (350-450 nm), than the light spectra in the habitats of P. h. chii. Conclusions: Two phylogenetically closely related bitterlings, P. h. himantegus and P. h. chii, dwell in different waters and exhibit different nuptial colorations and spectral sensitivities, which may be the results of speciation by sensory drive. Sensory ability and signal diversity accommodating photic environment may promote diversity of bitterling fishes. UV light was demonstrated to be a possible component of bitterling visual communication. The UV cue may assist bitterlings in gender identification.
Divergent Alanyl-tRNA Synthetase Genes of Vanderwaltozyma polyspora Descended from a Common Ancestor through Whole-Genome Duplication Followed by Asymmetric Evolution
(2015-07-01)
Chang, Chia-Pei
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Chang, Chih-Yao
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Lee, Yi-Hsueh
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Lin, Yeong-Shin
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Wang, Chien-Chia
Cytoplasmic and mitochondrial forms of a eukaryotic aminoacyl-tRNA synthetase (aaRS) are generally encoded by two distinct nuclear genes, one of eukaryotic origin and the other of mitochondrial origin. However, in most known yeasts, only the mitochondrial-origin alanyl-tRNA synthetase (AlaRS) gene is retained and plays a dual-functional role. Here, we present a novel scenario of AlaRS evolution in the yeast Vanderwaltozyma polyspora. Vanderwaltozyma polyspora possesses two significantly diverged AlaRS gene homologues, one encoding the cytoplasmic form and the other its mitochondrial counterpart. Clever selection of transcription and translation initiation sites enables the two isoforms to be localized and thus functional in their respective cellular compartments. However, the two isoforms can also be stably expressed and function in the reciprocal compartments by insertion or removal of a mitochondrial targeting signal. Synteny and phylogeny analyses revealed that the AlaRS homologues of Vanderwaltozyma polyspora arose from a dual-functional common ancestor through whole-genome duplication (WGD). Moreover, the mitochondrial form had higher synonymous (1.6-fold) and nonsynonymous (2.8-fold) substitution rates than did its cytoplasmic counterpart, presumably due to a lesser constraint imposed on components of the mitochondrial translational apparatus. Our study suggests that asymmetric evolution confers the divergence between the AlaRS paralogues of Vanderwaltozyma polyspora.
DNA barcode identification of fish products in Taiwan: Government-commissioned authentication cases
(2016-08)
Chang, Chia-Hao
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Lin, Han Yang
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Ren, Qiu
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Lin, Yeong-Shin
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Shao, Kwang-Tsao
Mislabeling of fish products not only impacts consumer finances, but can also be deleterious to public health. Fish products may be mislabeled for reasons including ambiguity of common fish names, challenging morphological identification, or willful intention to deceive. We reveal a high rate of mislabeling (70%) in 34 samples from 17 cases entrusted to us by three different Customs offices and one Coastal Patrol Office in Taiwan using DNA barcoding based on a partial segment of the mitochondrial cytochrome c oxidase subunit I gene (COI). In order to reduce the mislabeling of imported fish products, the authorities should take some actions into consideration, such as institutionalizating molecular authentication of fish products, standardizing the usage of common fish names, and legislating for penalties. (C) 2016 Elsevier Ltd. All rights reserved.
Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase
(2017-07-01)
Lee, Yi-Hsueh
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Chang, Chia-Pei
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Cheng, Yu-Ju
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Kuo, Yi-Yi
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Lin, Yeong-Shin
The discriminator base N73 is a key identity element of tRNA(His). In eukaryotes, N73 is an "A" in cytoplasmic tRNA(His) and a "C" in mitochondrial tRNA(His). We present evidence herein that yeast histidyl-tRNA synthetase (HisRS) recognizes both A73 and C73, but somewhat prefers A73 even within the context of mitochondrial tRNA(His). In contrast, humans possess two distinct yet closely related HisRS homologues, with one encoding the cytoplasmic form (with an extra N-terminal WHEP domain) and the other encoding its mitochondrial counterpart (with an extra N-terminal mitochondrial targeting signal). Despite these two isoforms sharing high sequence similarities (81% identity), they strongly preferred different discriminator bases (A73 or C73). Moreover, only the mitochondrial form recognized the anticodon as a strong identity element. Most intriguingly, swapping the discriminator base between the cytoplasmic and mitochondrial tRNA(His) isoacceptors conveniently switched their enzyme preferences. Similarly, swapping seven residues in the active site between the two isoforms readily switched their N73 preferences. This study suggests that the human HisRS genes, while descending from a common ancestor with dual function for both types of tRNA(His), have acquired highly specialized tRNA recognition properties through evolution.
Evolutionary information hidden in a single protein structure
(2012-06-01)
Shih, Chien-Hua
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Chang, Chih-Min
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Lin, Yeong-Shin
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Lo, Wei-Cheng
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Hwang, Jenn-Kang
The knowledge of conserved sequences in proteins is valuable in identifying functionally or structurally important residues. Generating the conservation profile of a sequence requires aligning families of homologous sequences and having knowledge of their evolutionary relationships. Here, we report that the conservation profile at the residue level can be quantitatively derived from a single protein structure with only backbone information. We found that the reciprocal packing density profiles of protein structures closely resemble their sequence conservation profiles. For a set of 554 nonhomologous enzymes, 74% (408/554) of the proteins have a correlation coefficient > 0.5 between these two profiles. Our results indicate that the three-dimensional structure, instead of being a mere scaffold for positioning amino acid residues, exerts such strong evolutionary constraints on the residues of the protein that its profile of sequence conservation essentially reflects that of its structural characteristics. Proteins 2012;. (c) 2012 Wiley Periodicals, Inc.
Global Investigation of Immune Repertoire Suggests Kawasaki Disease Has Infectious Cause
(2019-10-01)
Kuo, Ho-Chang
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Pan, Cheng-Tsung
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Huang, Ying-Hsien
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Huang, Fu-Chen
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Lin, Yeong-Shin
Background: Kawasaki disease (KD) severely threatens young children's health worldwide. The pathogenic mechanism of KD has not yet been solved, so there is still debate over whether KD is an infectious disease or an autoimmune disease. Methods and Results: To solve this problem, an immune repertoire analysis of KD was conducted. We collected blood cell RNA samples and prepared them into amplicons with iRepertoire kits. The amplicons were sequenced and analyzed with the iRepertoire pipeline. We first identified KD-specific VJ and VDJ forms that had the potential to serve as biomarkers of KD. In addition, the KD-specific VDJ forms were contributed mostly by immunoglobulin G. The D50 value analysis showed that B-cell diversity in KD is decreased, suggesting unique immunoglobulins are produced in KD. Moreover, V, D and J segment usage in IgA, IgG and IgM was consistent with previous KD studies. Further comparison showed no difference in CDR3 peptide length between KD and fever controls (subjects with fever but not diagnosed as KD), indicting KD had B-cell selection phenomenon that has a non-autoimmune pattern. The comparison of amino acid usage of the CDR3 region demonstrated a preference for hydrophilic amino acids in KD. Conclusions: The results of D50 value, VDJ usage and CDR3 peptide length analyses suggested the characteristics of infectious disease for KD.
Multiomics analyses identified epigenetic modulation of the S100A gene family in Kawasaki disease and their significant involvement in neutrophil transendothelial migration
(2018-11-01)
Huang, Lien-Hung
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Kuo, Ho-Chang
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Pan, Cheng-Tsung
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Lin, Yeong-Shin
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Huang, Ying-Hsien
BackgroundKawasaki disease (KD) is a prevalent pediatric disease worldwide and can cause coronary artery aneurysm as a severe complication. Typically, DNA methylation is thought to repress the expression of nearby genes. However, the cases in which DNA methylation promotes gene expression have been reported. In addition, globally, to what extent DNA methylation affects gene expression and how it contributes to the pathogenesis of KD are not yet well understood.MethodsTo address these important biological questions, we enrolled subjects, collected DNA and RNA samples from the subjects' total white blood cells, and performed DNA methylation (M450K) and gene expression (HTA 2.0) microarray assays.ResultsBy analyzing the variation ratios of CpG beta values (methylation percentage) and gene expression intensities, we first concluded that the CpG markers close (-1500bp to +500bp) to the transcription start sites had higher variation ratios, reflecting significant regulation capacities. Next, we observed that, globally speaking, gene expression was modestly negatively correlated (correlation rho approximate to-0.2) with the DNA methylation status of both upstream and downstream CpG markers in the promoter region. Third, we found that specific CpG markers were hypo-methylated in disease samples compared with healthy samples and hyper-methylated in convalescent samples compared with disease samples, promoting and repressing S100A genes' expressions, respectively. Finally, using an in vitro cell model, we demonstrated that S100A family proteins enhanced leukocyte transendothelial migration in KD.ConclusionsThis is the first study to integrate genome-wide DNA methylation with gene expression assays in KD and showed that the S100A family plays important roles in the pathogenesis of KD.
Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: Evidence for necessary taxonomic revision in the family and the identification of cryptic species
(2014-12-01)
Chang, Chia-Hao
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Li, Fan
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Shao, Kwang-Tsao
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Lin, Yeong-Shin
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Morosawa, Takahiro
Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships. In this study, we provide the most comprehensive phylogenetic reconstruction of species relationships of the group based on partitioned maximum likelihood and Bayesian methods using DNA sequence variation of nuclear and mitochondrial genes on 41 species, several subspecies and three undescribed species. Our findings support the monophyly of the Acheilognathidae. Two of the three currently recognized genera are not monophyletic and the family can be subdivided into six clades. These clades are further regarded as genera based on both their phylogenetic relationships and a reappraisal of morphological characters. We present a revised classification for the Acheilognathidae with five genera/lineages: Rhodeus, Acheilognathus (new constitution), Tanakia (new constitution), Paratanakia gen. nov., and Pseudorhodeus gen. nov. and an unnamed clade containing five species currently referred to as "Acheilognathus". Gene trees of several bitterling species indicate that the taxa are not monophyletic. This result highlights a potentially dramatic underestimation of species diversity in this family. Using our new phylogenetic framework, we discuss the evolution of the Acheilognathidae relative to classification, taxonomy and biogeography. (C) 2014 Elsevier Inc. All rights reserved.
Proportion of solvent-exposed amino acids in a protein and rate of protein evolution
(2007-04-01)
Lin, Yeong-Shin
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Hsu, Wei-Lun
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Hwang, Jenn-Kang
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Li, Wen-Hsiung
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生物科技學系
Translational selection, including gene expression, protein abundance, and codon usage bias, has been suggested as the single dominant determinant of protein evolutionary rate in yeast. Here, we show that protein structure is also an important determinant. Buried residues, which are responsible for maintaining protein structure or are located on a stable interaction surface between 2 subunits, are usually under stronger evolutionary constraints than solvent-exposed residues. Our partial correlation analysis shows that, when whole proteins are included, the variance of evolutionary rate explained by the proportion of solvent-exposed residues (P-exposed) can reach two-thirds of that explained by translational selection, indicating that P-exposed is the most important determinant of protein evolutionary rate next only to translational selection. Our result suggests that proteins with many residues under selective constraint (e.g., maintaining structure or intermolecular interaction) tend to evolve slowly, supporting the "fitness (functional) density" hypothesis.
Protein complexity, gene duplicability and gene dispensability in the yeast genome
(2007-01-31)
Lin, Yeong-Shin
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Hwang, Jenn-Kang
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Li, Wen-Hsiung
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生物科技學系
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Department of Biological Science and Technology
Using functional genomic and protein structural data we studied the effects of protein complexity (here defined as the number of subunit types in a protein) on gene dispensability and gene duplicability. We found that in terms of gene duplicability the major distinction in protein complexity is between hetero-complexes, each of which includes at least two different types of subunits (polypeptides), and homo-complexes, which include monomers and complexes that consist of only subunits of one polypeptide type. However, gene dispensability decreases only gradually as the number of subunit types in a protein complex increases. These observations suggest that the dosage balance hypothesis can explain well gene duplicability of complex proteins, but cannot completely explain the difference in dispensabilities between hetero-complex subunits. It is likely that knocking out a gene coding for a hetero-complex subunit would disrupt the function of the whole complex, so that the deletion effect on fitness would increase with protein complexity. We also found that multi-domain polypeptide genes are less dispensable but more duplicable than single-domain polypeptide genes. Duplicate genes derived from the whole genuine duplication event in yeast are more dispensable (except for ribosomal protein genes) than other duplicate genes. Further, we found that subunits of the same protein complex tend to have similar expression levels and similar effects of gene deletion on fitness. Finally, we estimated that in yeast the contribution of duplicate genes to genetic robustness against null mutation is similar to 9%, smaller than previously estimated. In yeast, protein complexity may serve as a better indicator of gene dispensability than do duplicate genes. (c) 2006 Elsevier B.V All rights reserved.
The complete mitochondrial genome of the big-eye thresher shark, Alopias superciliosus (Chondrichthyes, Alopiidae)
(2014-08-01)
Chang, Chia-Hao
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Shao, Kwang-Tsao
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Lin, Yeong-Shin
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Ho, Hsuan-Ching
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Liao, Yun-Chih
The complete mitochondrial genome of the big-eye thresher shark was sequenced using a polymerase chain reaction (PCR)-based method. The total length of mitochondrial DNA is 16,719 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the big-eye thresher shark is the same as the one observed in the most vertebrates. Base composition of the genome is A (31.8%), T (28.9%), C (25.8%) and G (13.5%).
The complete mitochondrial genome of the crocodile shark, Pseudocarcharias kamoharai (Chondrichthyes, Lamnidae)
(2016)
Chang, Chia-Hao
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Shao, Kwang-Tsao
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Lin, Yeong-Shin
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Ho, Hsuan-Ching
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生物科技學系
The complete mitochondrial genome of the crocodile shark consists of 16,688 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 replication origin region, and 1 control region. The mitochondrial gene arrangement of the crocodile shark is the same as that of most vertebrates. Base composition of the genome is A (32.0%), T (31.0%), C (23.7%) and G (13.3%).
The complete mitochondrial genome of the great white shark, Carcharodon carcharias (Chondrichthyes, Lamnidae)
(2014-10-01)
Chang, Chia-Hao
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Shao, Kwang-Tsao
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Lin, Yeong-Shin
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Fang, Yi-Chiao
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Ho, Hsuan-Ching
The complete mitochondrial genome of the great white shark having 16,744 bp and including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the great white shark is the same as the one observed in the most vertebrates. Base composition of the genome is A (30.6%), T (28.7%), C (26.9%) and G (13.9%).
The complete mitochondrial genome of the Rhodeus shitaiensis (Teleostei, Cypriniformes, Acheilognathidae)
(2015-04-01)
Li, Fan
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Shao, Kwang-Tsao
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Lin, Yeong-Shin
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Chang, Chia-Hao
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生物科技學系
The complete mitochondrial genome of the Rhodeus shitaiensis was determined by using a PCR-based method. The total length of mitochondrial DNA of this bitterling is 16,774 bp and includes 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region. The mitochondrial gene arrangement of the R. shitaiensis is also matching the one observed in the most vertebrate creatures. Base composition of the genome is A (28.7%), T (26.5%), C (27.4%) and G (17.4%) with an A+T rich hallmark as that of other vertebrate mitochondrial genomes.