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Evolutionary selection on synonymous codons in RNA G-quadruplex structural region 认领 引用
1
作者 Xu Yuming Qi Ting +1 位作者 Gu Wanjun Lu Zuhong 《Journal of Southeast University(English Edition)》 EI CAS 2021年第2期177-183,共7页
To investigate how synonymous codons have been adapted to the formation of ribonucleic acid(RNA)G-quadruplex(rG4)structure,a computational searching algorithm G4Hunter was applied to detect rG4 structures in protein-c... To investigate how synonymous codons have been adapted to the formation of ribonucleic acid(RNA)G-quadruplex(rG4)structure,a computational searching algorithm G4Hunter was applied to detect rG4 structures in protein-coding sequences of mRNAs in five eukaryotic species.The native sequences forming rG4s were then compared with randomized sequences to evaluate selection on synonymous codons.Factors that may influence the formation of rG4 were also investigated,and the selection pressures of rG4 in different gene regions were compared to explore its potential roles in gene regulation.The results show universal selective pressure acts on synonymous codons in rG4 regions to facilitate rG4 formation in five eukaryotic organisms.While G-rich codon combinations are preferred in the rG4 structural region,C-rich codon combinations are selectively unfavorable for rG4 formation.Gene's codon usage bias,nucleotide composition,and evolutionary rate can account for the selective variations on synonymous codons among rG4 structures within a species.Moreover,rG4 structures in the translational initiation region showed significantly higher selective pressures than those in the translational elongation region. 展开更多
关键词 ribonucleic acid(RNA)structure G-quadruplex synonymous codons evolution selection
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DISTRIBUTIONS OF TRIPLET CODONS IN MESSENGER RNA SECONDARY STRUCTURES 认领 引用 被引量：2
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作者 张静 顾宝洪 +1 位作者 彭守礼 刘次全 《Zoological Research》 1998年第5期350-358,共9页
Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational proper... Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein. 展开更多
关键词 Triplet codon Amino acid mRNA secondary structure
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mRNA Dependent Virtual-Real Substitutions of Nucleotides in Codons: The Dynamics of Their Meanings in the Genome Language 认领 引用
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作者 P. P. Gariaev E. A. Leonova-Gariaeva 《Open Journal of Genetics》 CAS 2019年第4期77-90,共14页
This is an attempt to explain mRNA-dependent non-stationary semantic values of codons (triplets) and nucleotides (letters) in codon composition during protein biosynthesis. This explanation is realized by comparing th... This is an attempt to explain mRNA-dependent non-stationary semantic values of codons (triplets) and nucleotides (letters) in codon composition during protein biosynthesis. This explanation is realized by comparing the different protein codes of various biosystem taxa, and, comparing mitochondrial code with the standard code. An initial mRNA transcriptional virtuality (Virtual-Reality) is transformed into material reality at the level of translation of virtual triplets into real (material) amino acids or into a real stop command of protein biosynthesis. The transformation of virtuality into reality occurs de facto when the linguistic sign1 functions of the codon syhoms are realized in the 3’ nucleotide (wobbling nucleotide according to F. Crick) in the process of protein biosynthesis. This corresponds to the theoretical works of the authors of this article. Despite the illusory appearance of semantic arbitrariness during the operation of ribosomes in the mode of codon semantic non-stationarity, this phenomenon probably provides biosystems with an unusually high level of adaptability to changes in the external environment as well as to internal (mental) dynamics of neuron’s genome in the cerebral cortex. The genome’s non-stationarity properties at the nucleotide, codon, gene and mental levels have fractal structure and corresponding dimensions. The highest form of such fractality (with maximum dimension) is probably realized in the genomic continuum of neurons in the human cerebral cortex through this semantic Virtual-to-Real (VR) codon transcoding with the biosynthesis of short-living semantic proteins, as the equivalents of material thinking-consciousness. In fact, this is the language of the brain’s genome, that is, our own language. In this case, the same thing happens in natural, primarily mental (non-verbal) languages. Their materialization is recorded in vocables (sounding words) and in writing. Such writing is the amino acid sequence in the semantic proteins of the human cerebral cortex. Rapidly decaying, such proteins can leave a long-lasting “so-called” Schr&#246;dinger wave holographic memory in the cerebral cortex. The presented below study is purely theoretical and based on a logical approach. The topic of the study is very complex and is subject to further development. 展开更多
关键词 Protein Biosynthesis Protein Codes Codons (Triplets) mRNA Virtual-Real (VR) Transcoding Semantics Thinking Consciousness
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Dependence of nucleotide physical properties on their placement in codons and determinative degree 认领 引用
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作者 BEREZHNOY A.Y. DUPLIJ S.A. 《Journal of Zhejiang University-SCIENCE B》 EI CAS 2005年第10期948-960,共13页
Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method num... Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (austin model 1) methods. As distinct from previous calculations, for nucleotides the interaction with neighbours is taken into account up to gradient of convergence equaling 1. The dependencies of these variables from the place in the codon and the de- terminative degree were obtained. The difference of these variables for codons and anticodons is shown. 展开更多
关键词 Dipole moment, Heat of formation, Total energy, DNA, Codon, Anticodon, Determinative degree
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Interaction of nonsense suppressor tRNAs and codon nonsense mutations or termination codons 认领 引用 被引量：1
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作者 Zixian Lu 《Advances in Biological Chemistry》 CAS 2012年第3期301-314,共14页
Codon nonsense mutations include amber, ochre, or opal mutations according to termination codon consisting of three types (TAG, TAA and TGA). Codon nonsense mutations are also divided into natural and artificial mutat... Codon nonsense mutations include amber, ochre, or opal mutations according to termination codon consisting of three types (TAG, TAA and TGA). Codon nonsense mutations are also divided into natural and artificial mutations. We discussed the interaction of codon nonsense mutations and suppressor tRNAs in vitro and in vivo. Nonsense suppressions do not only happen in prokaryotes but also in eukaryotes. Meanwhile, the misreading of termination codon and in-corporation of nonnatural amino acids into proteins are also introduced. 展开更多
关键词 Nonsense Suppression Codon Nonsense Mutation Suppressor tRNAs
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Codon Usage Bias in the Chloroplast Genome of the Traditional Chinese Medicinal Plant Corydalis yanhusuo 认领 引用
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作者 Bo Li Yuying Liang +2 位作者 Muqing He Xiuhe Fan Honghong Jiao 《Phyton-International Journal of Experimental Botany》 SCIE 2026年第3期131-147,共17页
This study aims to clarify the codon usage bias and influencing factors of protein-coding genes in the chloroplast genome of the medicinal plant Corydalis yanhusuo.The chloroplast genome sequence of C.yanhusuo was obt... This study aims to clarify the codon usage bias and influencing factors of protein-coding genes in the chloroplast genome of the medicinal plant Corydalis yanhusuo.The chloroplast genome sequence of C.yanhusuo was obtained by resequencing,approximately 50 protein-coding genes were screened,and the nucleotide composition and codon usage patterns were calculated and analyzed using CodonW 1.4.2 and EMBOSS software.The results showed that the total guanine and cytosine(GC)content of codons in the chloroplast genome of C.yanhusuo was 40.06%,and the GC contents at the third,second,and first codon positions(GC3,GC2,and GC1)were 32.12%,40.21%,and 47.84%,respectively,indicating that codons in the chloroplast genome of C.yanhusuo preferentially used adenine(A)or uracil(U).The effective number of codons(ENC)ranged from 42.87 to 61.00,with an average value of 50.54,indicating weak codon usage bias.A significant positive correlation existed between the GC content at the third codon position(GC3)and ENC,showing that codon bias was mainly affected by the third base.Neutral plot,ENC-plot,and PR2-plot analyses showed that the codon bias of the chloroplast genome of C.yanhusuo was mainly influenced by natural selection.Sixteen optimal codons—UUA,AUU,GUU,GUA,UCU,AGU,CCU,ACU,GCU,CAA,AAA,GAU,UGU,CGU,CGA,and GGU—were finally determined based on the relative synonymous codon usage analysis of high-frequency and highly expressed codons,all of which preferentially ended with A/U.Overall,this study reveals the codon usage bias of the chloroplast genome of C.yanhusuo and its influencing factors,and provides a theoretical basis for chloroplast genetic engineering and phylogenetic research. 展开更多
关键词 Corydalis yanhusuo Corydalis chloroplast genome codon usage bias optimal codons
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Plastome structure,divergence time,and C4 photosynthesis evolution in Chenopodiaceae s.s. 认领 引用
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作者 Shuai Liu Qiumei Cao +6 位作者 Giovanni Zecca Fabrizio Grassi Alexander P.Sukhorukov Mariyo Boboev Parvina Kurbonova Hikmat Hisoriev Zhibin Wen 《Journal of Systematics and Evolution》 SCIE CSCD 2026年第4期643-662,共20页
Chenopodiaceae s.s.(Amaranthaceae s.l.)contains the largest number of C4 species among eudicots.Despite this,plastome evolution within this family has been investigated in only a few species.Here,we analyzed 119 pl... Chenopodiaceae s.s.(Amaranthaceae s.l.)contains the largest number of C4 species among eudicots.Despite this,plastome evolution within this family has been investigated in only a few species.Here,we analyzed 119 plastomes from 115 species,including 78 newly sequenced plastomes,representing all subfamilies and most C4 lineages of Chenopodiaceae s.s.Plastome structural variants,rearrangements,and codon usage bias were compared across subfamilies and photosynthetic types.Multiple phylogenetic approaches were employed to reconstruct the evolutionary relationships within Chenopodiaceae s.s.,and Bayesian divergence time estimation was performed.Various Mk models for discrete character evolution were tested to investigate the evolution of C4 photosynthesis,and stochastic character mapping simulations were used to reconstruct shifts in photosynthetic pathways through time.Several plastome structural variants and rearrangements were identified,but associations with photosynthetic types were observed only in the subfamily Suaedoideae.Codon usage bias analysis revealed significant bias exclusively in C4 species,suggesting enhanced translational efficiency and accuracy as an adaptation to environmental conditions.We inferred multiple independent origins of the C4 pathway,with the oldest lineages—Bienertia(Suaedoideae)and Caroxyleae(Salsoloideae)—dating to approximately 34 and 32 million years ago(Ma),respectively,during the Oligocene.A marked increase in the number of C4 lineages occurred between 20 and 15 Ma.Declining atmospheric CO2 concentrations,combined with genetic,ecological,and environmental factors,likely promoted the expansion of C4 photosynthesis until recently.Finally,we identified five new hypervariable regions that will be valuable for phylogenetic and DNA barcoding applications in Chenopodiaceae s.s. 展开更多
关键词 C4photosynthesis Chenopodiaceae s.s. chloroplast genome codon bias evolution IR/SC boundary
Dietary arginine drives codon-dependent MHC class I translation and improves immunity in colon tumorigenesis and respiratory viral infection 认领 引用
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作者 Qiushuang Wu 《四川生理科学杂志》 2026年第8期1671-1671,共1页
Amino acid levels fluctuate across diverse pathological conditions.Whether such amino acid modulations directly shape pathophysiology by regulating host gene expression remains unknown.We found that extracellular argi... Amino acid levels fluctuate across diverse pathological conditions.Whether such amino acid modulations directly shape pathophysiology by regulating host gene expression remains unknown.We found that extracellular arginine restriction,observed in cancer and infection,represses specific arginine tRNAs-directly suppressing translation of major histocompatibility complex I(MHC class I)and antigen presentation.Arginine regulation of MHC class I was codon-usage dependent,as synonymous codon mutations prevented MHC class I modulation.Dietary arginine restriction impaired anti-viral immunity against influenza and SARS-CoV-2 and increased colon tumorigenesis.Conversely,increasing arginine availability via dietary supplementation or myeloid-specific arginase 1 deletion enhanced MHC class I protein levels,suppressed colon tumorigenesis,and improved viral infection outcomes.These disease modulating effects were abolished inβ2-microglobulin(B2m)-deficient mice.Thus,dietary modulation of a single amino acid critically influences codon-biased translation and MHC class I-mediated immunity to respiratory viral infections and cancer,revealing an unexpected mechanism and disease hazard for arginine deficiency and highlighting potential for amino acid-based translation modulation therapy. 展开更多
关键词 amino acid modulations amino acid regulating host gene expression synonymous codon mutations mhc class i dietary arginine major histocompatibility complex extracellular arginine restrictionobserved
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Prokaryotic expression of goldfish Tgf2 transposase with optimal codons and its enzyme activity 认领 引用 被引量：1
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作者 Xi Zhao Ruirui Si +2 位作者 Mingjuan He Xiayun Jiang Shuming Zou 《Aquaculture and Fisheries》 2019年第3期98-104,共7页
Tgf2 transposase(Tgf2-TPase),a hAT transposase from goldfish,plays an important role in fish transgenic applications.Previously,the production of the recombinant Tgf2-TPase protein required rigorous fermentation at lo... Tgf2 transposase(Tgf2-TPase),a hAT transposase from goldfish,plays an important role in fish transgenic applications.Previously,the production of the recombinant Tgf2-TPase protein required rigorous fermentation at low temperatures(22℃)and early log phase induction(OD600=0.3–0.4)in Rosetta 1(DE3)Escherichia coli lines.In order to better express the Tgf2-TPase and detect its enzyme activity,83 rare codons in Tgf2-TPase were optimized and designated Tgf2-TPase83.The expression results showed that the soluble recombinant Tgf2-TPase83 was highly expressed at 30℃ and was inducible at an OD600 of 0.5–0.6 in the same prokaryotic expression system.After purification by affinity chromatography,Tgf2-TPase83 with codon optimization had higher enzyme activity than the Tgf2-TPase control.Comparison of different preservation methods(freezedrying at−80℃,storage in 20%-glycerol,8%-sucrose,4%-mannitol),revealed storage of Tgf2-TPase83 in glycerol helped to preserve its DNase digestion activity.Furthermore,size exclusion chromatography suggested that the purified Tgf2-TPase83 could recognize and bind to DNA probes containing a terminal inverted repeat(TIR)and a subterminal repeat(STR)sequence of the Tgf2 transposon.Overall,the results showed that optimizing the 83 codons of Tgf2 transposase can simplify the fermentation process and improve the enzyme activity.We propose that the production of the Tgf2-Tpase83 protein in a soluble and active form could provide an alternative tool for genetic modification of fish. 展开更多
关键词 Codon optimization Enzyme activity Prokaryotic expression Tgf2 transposase
The variable codons of H5N1 avian influenza A virus haemagglutinin genes 认领 引用
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作者 Mark J.GIBBS Robert W.MURPHY 《Science China(Life Sciences)》 CAS 2008年第11期987-993,共7页
We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 19... We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 1997 to 2007, except viruses from 2000. The haemagglutinin sequences of viruses from southeast Asia, Hong Kong and China's Mainland were the most polymorphic and had similar nonsyn-onymous profiles. Some sites were positively selected in viruses from most regions and a few of these sites displayed different amino acid patterns. Selection appeared to produce different outcomes in vi-ruses from Europe, Africa and Russia and from different host types. One position was found to be positively selected for human isolates only. Although the functions of some positively selected posi-tions are unknown, our analysis provided evidence of different temporal, spatial and host adaptations for H5N1 avian influenza viruses. 展开更多
关键词 positive selection pressure H5N1 avian influenza virus HA codon
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A premature termination codon mutation in the onion AcCER2 gene is associated with both glossy leaves and thrip resistance 认领 引用 被引量：1
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作者 Pengzheng Lei Meihong Pan +11 位作者 Shiqiang Kang Peng Zeng Yu Ma Yingmei Peng Xiushan Ma Wei Chen Linyu He Haifeng Yang Weiya Li Shilin Zhang Linchong Hui Jing Cai 《Horticulture Research》 SCIE CSCD 2025年第4期242-254,共13页
Plant epicuticular waxes(EW)play a critical role in defending against biotic and abiotic stresses.Notably,onions(Allium cepa L.)present a distinctive case where the mutant with defect in leaf and stalk EW showed resis... Plant epicuticular waxes(EW)play a critical role in defending against biotic and abiotic stresses.Notably,onions(Allium cepa L.)present a distinctive case where the mutant with defect in leaf and stalk EW showed resistance to thrips compared with the wild type with integral EW.We identified a premature stop codon mutation in the AcCER2 gene,an ortholog of CER2 gene in Arabidopsis thaliana that has been proved essential for the biosynthesis of very long-chain fatty acids(VLCFAs),in the onions with glossy leaf and stalks in our experiments.The data hinted at the possibility that this mutation might impede the elongation process of VLCFAs from C28 to C32,thereby hindering the production of 16-hentriacontanone,a primary constituent of onion EW.Transcriptomic analysis revealed substantial alterations in expression of genes in the pathways related not only to lipid synthesis and transport but also to signal transduction and cell wall modification in glossy mutants.Meanwhile,metabolomic profiling indicates a remarkable increase in flavonoid accumulation and a significant reduction in soluble sugar content in glossy mutants.These findings suggested that the enhanced resistance of glossy mutants to thrips might be a consequence of multiple physiological changes,and our integrated multiomics analysis highlighting the regulatory role of AcCER2 in these processes.Our study has yielded valuable insights into the biosynthesis of onion EW and has provided an initial hypothesis for the mechanisms underlying thrip resistance.These findings hold significant promise for the breeding programs of thrip-resistant onion. 展开更多
关键词 defending biotic abiotic stressesnotablyonions allium premature stop codon mutation glossy leaves onion accer gene cer gene accer genean plant epicuticular waxes ew play arabidopsis thaliana
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Complete Genomic Sequence Analysis of Sweet Potato Virus 2 Isolates from the Shandong and Jiangsu Provinces in China 认领 引用
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作者 Zichen Li Jukui Ma +2 位作者 Minjun Liu Guowei Geng Hongxia Zhang 《Phyton-International Journal of Experimental Botany》 SCIE 2025年第6期1841-1856,共16页
Sweet potatoes are significant cash crops,however,their yield and quality are greatly compromised by viral diseases.In this study,the complete genomic sequences of two Sweet Potato Virus 2(SPV2)isolates from infected ... Sweet potatoes are significant cash crops,however,their yield and quality are greatly compromised by viral diseases.In this study,the complete genomic sequences of two Sweet Potato Virus 2(SPV2)isolates from infected sweet potato leaves in the Shandong(designated as SPV2-SDYT,GenBank No.PQ855660.1)and Jiangsu(designated as SPV2-JSXZ,GenBank No.PQ855661.1)provinces in China were obtained using 5′RACE and RT-PCR amplification.Consistency,phylogeny,codon usage bias,recombination,and selection pressure analyses were conducted using the SPV2-SDYT and SPV2-JSXZ genome sequences.The complete genome sequences of SPV2-SDYT and SPV2-JSXZ were 10561 nucleotides(nt)in length,with respective nucleotide and amino acid identities of 99.25%and 99.12%,respectively.Both isolates were closely related to the SPV2 isolate from China(SPV2-LN).In both SPV2-SDYT and SPV2-JSXZ,the identity of the P1 protein was the highest,whereas that of the P3 protein was the lowest.There were 26 codons with relatively synonymous codon usage(RSCU)values greater than 1 in SPV2-SDYT and 27 codons with RSCU values greater than 1 in SPV2-JSXZ.High-frequency codons in their genomes were predominantly found to end with A/U.Recombination analysis revealed no major recombination sites in either SPV2-SDYT or SPV2-JSXZ.Further selection pressure analysis showed that the non-synonymous substitution rate/synonymous substitution rate(dN/dS)value of all 10 SPV2 proteins was less than 1.This is the first report on the evolutionary relationships of the 17 known SPV2 isolates.Our findings lay the molecular groundwork for preventing and controlling SPV2 infection in root-tuber crops.These findings also contribute to our understanding of the spread and evolution of SPV2,its pathogenic mechanisms,and the development of antiviral strategies against it. 展开更多
关键词 Sweet potato virus 2 consistency analysis phylogenetic analysis codon usage bias analysis recombination analysis selection pressure analysis
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A Genome-wide Analysis of the 14-3-3 Gene Family in Chinese Chestnut(Castanea mollissima) 认领 引用
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作者 Xiaoxiao KANG Yaming LIU +1 位作者 Liying FAN Hai'e ZHANG 《Agricultural Biotechnology》 2025年第6期1-9,共9页
[Objectives]The 14-3-3 proteins are a class of highly conserved adapter proteins in eukaryotes that play a central role in signal transduction by recognizing phosphorylated target proteins and are crucial for plant gr... [Objectives]The 14-3-3 proteins are a class of highly conserved adapter proteins in eukaryotes that play a central role in signal transduction by recognizing phosphorylated target proteins and are crucial for plant growth and development.Chinese chestnut(Castanea mollissima)is an important woody grain crop in China.This study aimed to systematically identify the 14-3-3 gene family in chestnut and investigate their fundamental characteristics and functional clues,thereby laying a foundation for further elucidating the biological functions of this family in Chinese chestnut.[Methods]Using a combination of bioinformatics and molecular biology approaches,we conducted a comprehensive identification of the 14-3-3 family members in Chinese chestnut.Subsequently,we systematically analyzed their physicochemical properties,gene structures,conserved domains and motifs,gene duplication events,phylogenetic relationships,tissue-specific expression patterns,and codon usage bias.[Results]A total of nine 14-3-3 family members,designated CmGRF1 to CmGRF9,were identified and classified into two subgroups:epsilon(5 members)and non-epsilon(4 members).All CmGRF proteins were predicted to be hydrophilic.Phylogenetic analysis revealed a strong correlation between the clustering of CmGRFs and their respective gene structures,conserved domains,and motif compositions.Transcriptome data analysis indicated significant differences in the expression levels of different CmGRF members across various tissues and developmental stages.Codon preference analysis showed that CmGRFs tend to use codons ending with A/U,and their evolution is primarily driven by natural selection pressure.[Conclusions]This study provides the first genome-wide systematic analysis of the gene family in Chinese chestnut.The findings offer important theoretical insights and candidate genes for further research into the specific functions of these family members in chestnut growth,development,and stress responses. 展开更多
关键词 Chinese chestnut 14-3-3 gene family Phylogenetic analysis Codon usage bias
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Genome-Wide Patterns of Codon Usage in the Pacific Oyster Genome 认领 引用 被引量：1
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作者 SONG Kai 《Journal of Ocean University of China》 SCIE CAS CSCD 2021年第5期1175-1182,共8页
The use of synonymous codons with varying frequencies has been observed in many species,and the magnitude varies among closely related species and genes within the same genome.Mutational processes or natural selective... The use of synonymous codons with varying frequencies has been observed in many species,and the magnitude varies among closely related species and genes within the same genome.Mutational processes or natural selective pressures affect this bias.However,a systematic investigation of codon usage pattern for molluscan species and its association with the two factors hasn’t been conducted.In this study,the whole genome codon usage patterns in oyster genome is investigated using the relative synonymous codon usage(RSCU)method,and 17 putative optimal codons were identified,wherein most had either a cytosine(C)or guanine(G)residue at the third position.Results showed that codon bias was positively associated with gene expression levels and breadth.Optimal codons had different mutational bias patterns compared with nonoptimal codons.Moreover,the results show that codon bias is negatively associated with nucleotide diversity.In the oyster genome,the fourfold degenerate codons are affected by different selective pressures,which can be regarded as an evidence that natural selection shapes codon usage patterns.This research will help to understand how natural selection and mutation bias affect codon usage in Mollusca genomes. 展开更多
关键词 codon bias synonymous codons gene expression nucleotide diversity Crassostrea gigas
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Genomic Landscape of Rare Codon Usage at Start Region in the Pacific Oyster Genome 认领 引用
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作者 SONG Kai 《Journal of Ocean University of China》 SCIE CAS CSCD 2023年第4期1041-1048,共8页
Synonymous codons have different frequencies of usage in many species.Based on the frequency of usage,the codons can be divided into two groups,rare codons and abundant codons.Rare codons are found to be enriched at t... Synonymous codons have different frequencies of usage in many species.Based on the frequency of usage,the codons can be divided into two groups,rare codons and abundant codons.Rare codons are found to be enriched at the start regions of genes,and it is assumed that these codons can reduce elongation speed of genes.However,the rare codon usage in different genomic regions of mollusks and their relationship with selective pressure has not been systematically investigated.In this study,the patterns of rare codon usage are characterized at whole genome level,and their relationship with selective pressures is investigated in Crassostrea gigas.The rare codons are enriched at the start regions of genes with high and medium expression levels,and their proportion is higher than those in the genes with low expression level.The genes with longer coding sequences and more exon numbers have lower fraction of rare codons at start regions.Rare codons have lower level of nucleotide diversity and higher frequency of rare mutations at start regions.This work is the first comprehensive investigation of the relationships between rare codon usage and some intrinsic genetic factors in mollusca species.The results suggest that the selective pressures play an important role in shaping the rare codon usage in the C.gigas genome. 展开更多
关键词 rare codons selective pressures nucleotide diversity Crassostrea gigas
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Chloroplast genomes of key species shed light on the evolution of the ancient genus Isoetes 认领 引用 被引量：2
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作者 Jovani B.S.Pereira Ana Maria Giulietti +5 位作者 Eder S.Pires Marcele Laux Maurício T.C.Watanabe Renato R.M.Oliveira Santelmo Vasconcelos Guilherme Oliveira 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2021年第3期429-441,共13页
Although phylogenetic studies have revealed major clades,the deepest relationships in Isoetes remain unresolved.The use of next-generation sequencing provides enormous amounts of gene sequences,which allows not only c... Although phylogenetic studies have revealed major clades,the deepest relationships in Isoetes remain unresolved.The use of next-generation sequencing provides enormous amounts of gene sequences,which allows not only clarification of the basal relationships but also rapid radiations.Plastomes of six key Isoetes species were annotated,revealing a total of 129 or 130 genes,depending on the species.Our phylogenomic analyses comprising representatives of all major clades yielded well-supported nodes and identical topologies using maximum likelihood and Bayesian inference.The phylogenetic reconstructions detangled the deep relationships in Isoetes and illuminated the more recent radiations in the genus.A basal dichotomy was found that grouped Isoetes spp.from Brazil and South Africa into a clade sister to the remaining Isoetes groups.Interestingly,I.andicola was found to be sister to the North American species complex.Genomic trait mapping analysis showed that the missing introns in the atpF and clpP genes were well conserved in two major clades.The absence of trnK-UUU was observed in the Brazilian tropical species and in I.velata.Among lycophytes,the gene trnR-CCG was missing only in I.eludens.In general,genomic traits such as the presence or absence of internal stop codons,a tRNA,and an intron were revealed to be conserved within groups,suggesting that these genomic traits might reveal vital information about the evolution of the genus.This study will contribute to understanding the diversification of Isoetes and the establishment of a better framework to address the evolutionary history of the genus. 展开更多
关键词 internal stop codons Isoetes lycophytes next-generation sequencing phylogenomic RNA editing tRNA
Hepatitis B virus genotypes and genome characteristics in China 认领 引用 被引量：45
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作者 Hong-Mei Li Jian-Qiong Wang +4 位作者 Rui Wang Qian Zhao Li Li Jin-Ping Zhang Tao Shen 《World Journal of Gastroenterology》 SCIE CAS 2015年第21期6684-6697,共14页
AIM:To analyze the hepatitis B virus(HBV) characters in China,as well as the correlation between several HBV mutation and hepatitis symptoms.METHODS:A total of 1148 HBV genome sequences from patients throughout China ... AIM:To analyze the hepatitis B virus(HBV) characters in China,as well as the correlation between several HBV mutation and hepatitis symptoms.METHODS:A total of 1148 HBV genome sequences from patients throughout China were collected via the National Center For Biotechnology Information database(information including:genotype,territory and clinical status).HBV genotypes were classified by a direct reference from the Genbank sequence annotation,phylogenetic tree and online software analysis(http://gffzz16a62c593b5540cehkooq5knc9f9565xu.ffgz.tsg.suse.edu.cn/projects/genotyping/formpage.cgi).The phylogenetic tree was constructed based on the neighbor-joining method by MEGA5.0 software.HBV sequences were grouped based on phylogenetic tree and the distance between the groups was calculated by using the computer between group mean distance methods.Seven hundred and twelve HBV sequences with clear annotation of clinical symptoms were selected to analyses the correlation of mutation and clinical symptoms.Characteristics of sequences were analyzed by using DNAStar and BioEdit software packages.The codon usage bias and RNA secondary structures analysis were performed by RNAdraw software.Recombination analysis was performed by using Simplot software.RESULTS:In China,HBV genotype C was the predominant in Northeastern,genotype B was predominant in Central Southern areas,genotype B and C were both dominant in Southwestern areas,and the recombinant genotype C/D was predominant in Northwestern areas.C2 and B2 were identified as the two major sub-genotypes,FJ386674 might be a putative sub-genotype as B10.The basal core promoter double mutation and pre-C mutation showed various significant differences between hepatitis symptoms.In addition to ATG,many other HBV initiation codons also exist.HBV has codon usage bias;the termination codon of X,C and P open reading frames(ORF) were TAA,TAG,and TGA,respectively.The major stop codons of S-ORF were TAA(96.45%) and TGA(83.60%) in B2 and C2 subtype,respectively.CONCLUSION:This study recapitulated the epidemiology of HBV in China,and the information might be meaningful critical for the future prevention and therapy of HBV infections. 展开更多
关键词 Hepatitis B virus Genotype Phylogenetictree Clinical symptoms Mutation Codon usage bias
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Genome-wide analysis of the synonymous codon usage patterns in apple 认领 引用 被引量：13
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作者 LI Ning SUN Mei-hong +2 位作者 JIANG Ze-sheng SHU Huai-rui ZHANG Shi-zhong 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2016年第5期983-991,共9页
Apple（Malus×domestica） has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent oppo... Apple（Malus×domestica） has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by Codon W and SPSS（Statistical Product and Service Solutions） programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also influence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple. 展开更多
关键词 apple the synonymous codon usage patterns codon bias RSCU
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Synonymous codon usage pattern in model legume Medicago truncatula 认领 引用 被引量：11
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作者 SONG Hui LIU Jing +1 位作者 CHEN Tao NAN Zhi-biao 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2018年第9期2074-2081,共8页
Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes... Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula. In present study, 39 531 available coding sequences （CDSs） from M. truncatula were examined for codon usage bias （CUB）. Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB. We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage. These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively. Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs. The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content. Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop. 展开更多
关键词 codon usage gene expression Medicago truncatula natural selection optimal codon
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p53 codon 72 polymorphism and liver cancer susceptibility:A meta-analysis of epidemiologic studies 认领 引用 被引量：8
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作者 Xi Chen Fei Liu +3 位作者 Bo Li Yong-Gang Wei Lv-Nan Yan Tian-Fu Wen 《World Journal of Gastroenterology》 SCIE CAS CSCD 2011年第9期1211-1218,共8页
AIM:To evaluate the association between p53 codon 72 polymorphism and liver cancer risk by means of meta-analysis.METHODS:Two investigators independently searched the Medline,Embase and Chinese Biomedicine databases.S... AIM:To evaluate the association between p53 codon 72 polymorphism and liver cancer risk by means of meta-analysis.METHODS:Two investigators independently searched the Medline,Embase and Chinese Biomedicine databases.Summary odds ratios and 95%CI for p53 codon 72 polymorphism and liver cancer were calculated in fixedeffects model(Mantel-Haenszel method)and randomeffects model(DerSimonian and Laird method)when appropriate.RESULTS:This meta-analysis included 1115 liver cancer cases and 1778 controls.The combined results based on all studies showed that there was a statistically significant link between Pro/Pro genotype and liver cancer,but not between Arg/Arg or Pro/Arg genotype and liver cancer.When stratifying for race,similar results were obtained,i.e.patients with liver cancer had a significantly higher frequency of Pro/Pro genotype than non-cancer patients among Asians.After stratifying thevarious studies by control source,gender,family history of liver cancer and chronic hepatitis virus infection,we found that(1)patients among hospital-based studies had a significantly higher frequency of Pro/Pro and a significantly lower frequency of Arg/Arg genotype than individuals without cancer;(2)female patients with liver cancer had a significantly lower frequency of Arg/Arg and a higher frequency of Pro/Arg+Pro/Pro genotypes than female individuals without cancer;(3)subgroup analyses for family history of liver cancer did not reveal any significant association between p53 codon 72 polymorphism and liver cancer development;and(4)patients with negative hepatitis virus infection had a significantly higher frequency of Pro/Pro and a significantly lower frequency of Arg/Arg genotype than individuals without cancer.CONCLUSION:This meta-analysis suggests that the p53 codon 72 polymorphism may be associated with liver cancer among Asians. 展开更多
关键词 Liver cancer p53 codon 72 Gene polymorphism Meta-analysis
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