Background:A thorough examination of the physicochemical properties,higher-order structure,subcellular localization,and selective pressure of the cytochrome c oxidase subunit I(COX1)protein of the endemic species Eoth...Background:A thorough examination of the physicochemical properties,higher-order structure,subcellular localization,and selective pressure of the cytochrome c oxidase subunit I(COX1)protein of the endemic species Eothenomys miletus(E.miletus)in the Hengduan Mountains provides further insights into molecular characteristics and function of the COX1 gene in E.miletus.Method:The physicochemical properties and higher-order structure of the COX1 protein of E.miletus were analyzed using bioinformatics software.Subsequently,a phylogenetic tree was constructed using Mega 7.0 software based on the COX1 gene from 19 species of the Arvicolinae subfamily and 3 species of the Muridae.Selection pressure analysis was performed using the PAML 4.7 software and the Datamonkey online website.Results:The COX1 protein of E.miletus comprises/consists of 514 amino acids,with leucine(Leu/L)being the most prevalent amino acid(11.5%).This hydrophilic protein contains 42 phosphorylation sites and 4 N-glycosylation sites.It possesses a transmembrane domain and lacks signal peptide distribution,thus classifying it as a non-GPI-anchored protein.The secondary structure of the COX1 protein consists ofα-helices(36.77%),random coils(33.85%),and extended chains,a composition consistent with/findings that align with its tertiary structure.Significant genetic differentiation exists among species within the Arvicolinae subfamily,a finding consistent with morphological identification results.The COX1 gene in Arvicolinae species exhibits purifying selection.Conclusion:This study analyzed the physicochemical properties of the COX1 protein in E.miletus.Phylogenetic and selection pressure analyses reveal significant genetic divergence among Arvicolinae species,and demonstrate that the COX1 gene is evolutionarily conserved within the Arvicolinae subfamily.展开更多
[Objective]The aim was to research the relationship between nucleotide substitutions rate and selective pressure.[Method]Synonymous and nonsynonymous substitutions and their ratios for some sorghum and maize genes in ...[Objective]The aim was to research the relationship between nucleotide substitutions rate and selective pressure.[Method]Synonymous and nonsynonymous substitutions and their ratios for some sorghum and maize genes in nucleus and organelle genomes were analyzed by statistical method,and comparative analysis of related functional genes were carried out.[Result]The pure selective pressures of the related functional genes were similar between nucleus and chloroplast genomes,but was lower in mitochondrial genome.The significant differences of nucleotide substitution rate between sorghum and maize orthologous genes in nucleus genome,and among different functional genes in nucleus genome were mainly due to the nonsynonymous substitution difference.[Conclusion]The molecular evolutional rate of different functional genes and different lineages were influenced by selective pressure.The differences of molecular evolutional rate among nucleus,chloroplast and mitochondria genomes had no direct relationship with selective pressure.展开更多
A novel method based on the selective pressure of particle size （particle-size cultivation method, PSCM） was developed for the cultivation and operation of aerobic granular sludge in a continuous-flow reactor, and c...A novel method based on the selective pressure of particle size （particle-size cultivation method, PSCM） was developed for the cultivation and operation of aerobic granular sludge in a continuous-flow reactor, and compared with the conventional method based on the selective pressure of settling velocity （settling-velocity cultivation method, SVCM）. Results indicated that aerobic granules could be cultivated in continuous operation mode by this developed method within 14 days. Although in the granulation process, under particle-size selective pressure, mixed liquor suspended solids （MLSS） in the reactor fluctuated greatly and filamentous bacteria dominated the sludge system during the initial operation days, no obvious difference in profile was found between the aerobic granules cultivated by PSCM and SVCM. Moreover, aerobic granules cultivated by PSCM presented larger diameter, lower water content and higher specific rates of nitrification, denitrifieation and phosphorus removal, but lower settling velocity. Under long term operation of more than 30 days, aerobic granules in the continuous-flow reactor could remain stable and obtain good chemical oxygen demand （COD）, NH4^＋-N, total nitrogen （TN） and total phosphorus （TP） removal. The results indicate that PSCM was dependent on the cultivation and maintenance of the stability of aerobic granules in continuous-flow bioreactors.展开更多
KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences.Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences,...KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences.Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences,selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences.As testified on empirical data,KaKs_Calculator 3.0 shows effectiveness to detect the strength and mode of selection operated on molecular sequences,accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at a whole-genome scale.The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.展开更多
To study the quasispecies diversity of porcine reproductive and respiratory syndrome virus (PRRSV), open reading frame 5 (ORF5) of strain SD0612 was amplified and cloned. Sixty clones of ORF5 were sequenced and analyz...To study the quasispecies diversity of porcine reproductive and respiratory syndrome virus (PRRSV), open reading frame 5 (ORF5) of strain SD0612 was amplified and cloned. Sixty clones of ORF5 were sequenced and analyzed with DNAStar software. Nucleic acid sequence homology was 97.7%-100%, with 78 mutations observed. Among these 60 clones, the sequences of 17 clones were identical and recognized as the dominant quasispecies of strain SD0612. Evolution of SD0612 quasispecies diversity under antibody selective pressure was also studied. SD0612 was passed continuously in the Marc-145 cell line over 40 passages in 6 independent lineages. SD0612 antiserum was not added to lineage A, B, and C cultures; however, antiserum was added to culture medium for lineages D, E, and F. PRRSV ORF5 was then amplified, cloned, and sequenced from each of the 6 lineages, designated as A40-F40. F40 was further passed in Marc-145 cells using 6 independent lineages with or without F40 antiserum for another 40 passages. ORF5 from the 6 newly-derived virus lineages, which we designated as a40-f40, were amplified, cloned and sequenced. The proportion of dominant quasispecies increased with passage number in cell cultures supplemented with antibodies, but decreased when antibodies were lacking. Our work has demonstrated a diversity of quasispecies for ORF5 in PRRSV SD0612. Antibody selective pressure was able to significantly influence quasispecies diversity and promote a dominant quasispecies that was able to evade immune reactions.展开更多
Birds,a fascinating and diverse group occupying various habitats worldwide,exhibit a wide range of life-history traits,reproductive methods,and migratory behaviors,all of which influence their immune systems.The assoc...Birds,a fascinating and diverse group occupying various habitats worldwide,exhibit a wide range of life-history traits,reproductive methods,and migratory behaviors,all of which influence their immune systems.The association between major histocompatibility complex(MHC)genes and certain ecological factors in response to pathogen selection has been extensively studied;however,the role of the co-working molecule T cell receptor(TCR)remains poorly understood.This study aimed to analyze the copy numbers of TCR-V genes,the selection pressure(ωvalue)on MHC genes using available genomic data,and their potential ecological correlates across 93 species from 13 orders.The study was conducted using the publicly available genome data of birds.Our findings suggested that phylogeny influences the variability in TCR-V gene copy numbers and MHC selection pressure.The phylogenetic generalized least squares regression model revealed that TCR-Vαδcopy number and MHC-I selection pressure were positively associated with body mass.Clutch size was correlated with MHC selection pressure,and Migration was correlated with TCR-Vβcopy number.Further analyses revealed that the TCR-Vβcopy number was positively correlated with MHC-IIB selection pressure,while the TCR-Vγcopy number was negatively correlated with MHC-I peptide-binding region selection pressure.Our findings suggest that TCR-V diversity is significant in adaptive evolution and is related to species’life-history strategies and immunological defenses and provide valuable insights into the mechanisms underlying TCR-V gene duplication and MHC selection in avian species.展开更多
Mitochondria play a key role in lipid metabolism,and mitochondrial DNA(mtDNA)mutations are thus considered to affect obesity susceptibility by altering oxidative phosphorylation and mitochondrial function.In this stud...Mitochondria play a key role in lipid metabolism,and mitochondrial DNA(mtDNA)mutations are thus considered to affect obesity susceptibility by altering oxidative phosphorylation and mitochondrial function.In this study,we investigate mtDNA variants that may affect obesity risk in 2877 Han Chinese individuals from 3 independent populations.The association analysis of 16 basal mtDNA haplogroups with body mass index,waist circumference,and waist-to-hip ratio reveals that only haplogroup M7 is significantly negatively correlated with all three adiposity-related anthropometric traits in the overall cohort,verified by the analysis of a single population,i.e.,the Zhengzhou population.Furthermore,subhaplogroup analysis suggests that M7b1a1 is the most likely haplogroup associated with a decreased obesity risk,and the variation T12811C(causing Y159H in ND5)harbored in M7b1a1 may be the most likely candidate for altering the mitochondrial function.Specifically,we find that proportionally more nonsynonymous mutations accumulate in M7b1a1 carriers,indicating that M7b1a1 is either under positive selection or subject to a relaxation of selective constraints.We also find that nuclear variants,especially in DACT2 and PIEZO1,may functionally interact with M7b1a1.展开更多
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
G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world ...G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world is the result of natural selection for functionality. In this study, we identified putative quadruplex-forming sequences(PQSs) across the known viral genomes and analyzed the abundance, structural stability, and conservation of viral PQSs. A Viral Putative G-quadruplex Database(http://jsjds.hzau.edu.cn/MBPC/Vi PGD/index.php/home/index) was constructed to collect the details of each viral PQS, which provides guidance for selecting the desirable PQS. The PQS with two putative G-tetrads(G2-PQS) was significantly enriched in both eukaryotic viruses and prokaryotic viruses, whereas the PQSs with three putative G-tetrads(G3-PQS) were only enriched in eukaryotic viruses and depleted in prokaryotic viruses. The structural stability of PQSs in prokaryotic viruses was significantly lower than that in eukaryotic viruses. Conservation analysis showed that the G2-PQS, instead of G3-PQS, was highly conserved within the genus. This suggested that the G2-quadruplex might play an important role in viral biology, and the difference in the occurrence of G-quadruplex between eukaryotic viruses and prokaryotic viruses may result from the different selection pressures from hosts.展开更多
Positive selection and differential selective pressure analyses were carried out to study Haemagglutinin (HA) genes of H9N2 influenza viruses from different hosts in this paper. Results showed that, although most posi...Positive selection and differential selective pressure analyses were carried out to study Haemagglutinin (HA) genes of H9N2 influenza viruses from different hosts in this paper. Results showed that, although most positions in HAs were under neutral or purifying evolution, a few positions located in the antigenic regions and receptor binding sites were subject to positive selection and some of them were even positively selected at the population level. In addition, there were always some positions differentially selected for viruses from different hosts. Both selection pressure working on HA codons and positions differentially selected might account for the extension of the host range and adaptations to different hosts of H9N2 influenza viruses.展开更多
AIM： To evaluate the efficacy of selective laser trabeculoplasty（SLT） in glaucomatous eyes with previous incisional glaucoma surgery. METHODS： A retrospective cohort of eyes that underwent SLT at a single institut...AIM： To evaluate the efficacy of selective laser trabeculoplasty（SLT） in glaucomatous eyes with previous incisional glaucoma surgery. METHODS： A retrospective cohort of eyes that underwent SLT at a single institution from 2013-2015 were followed for 1 y. Reduction in intraocular pressure（IOP） following SLT was evaluated in eyes with prior trabeculectomy with Ex Press mini shunt（Alcon, Ft Worth, TX, USA）, Ahmed valve（New World Medical, Cucamonga, CA, USA）, or combined phacoemulsification-trabeculectomy. A control group was included with eyes without prior surgery that underwent SLT. Success was defined as 〉20% drop in IOP from pre-SLT baseline. RESULTS： One-hundred and six eyes were included with 53 in both the prior glaucoma surgery（PGS） and no prior glaucoma surgery（NPGS） groups. Mean pre-SLT IOP was 19.2±4.3 and 20.6±6.0 mm Hg for PGS and NPGS groups, respectively（P=0.17）. Both groups produced statistically significant IOP reductions at 1 and 6 mo（P〈0.04）. At 6 mo, mean IOP reduction reached 7.3% and 10.8% for the PGS and NPGS groups, respectively（P=0.42）. Overall, 27.9% and 31.7% of eyes in PGS and NPGS groups met success criteria at 1 y（P=0.70）. In the PGS group, eyes with baseline IOP ≥21 mm Hg had IOP reductions of 18.1%（P〈0.001）, 16.7%（P〈0.01）, and 8.4%（P=0.31） compared to eyes with baseline IOP 〈21 mm Hg who had IOP reductions of 2.3%（P=0.39）, 3.4%（P=0.19）, and 1.1%（P=0.72） at 1, 6 mo, and 1 y, respectively. CONCLUSION： SLT is efficacious in eyes with prior incisional glaucoma surgery and results in similar IOP reductions compared to eyes without PGS. A larger IOP reduction is observed following SLT in eyes with higher pre-SLT IOP.展开更多
Black rockfish(Sebastes schlegelii)has evolved viviparous reproduction mode.Different from the oviparous fishes,the spermatozoa of black rockfish are stored on the surface of ovarian follicle for over four months unti...Black rockfish(Sebastes schlegelii)has evolved viviparous reproduction mode.Different from the oviparous fishes,the spermatozoa of black rockfish are stored on the surface of ovarian follicle for over four months until the egg mature in ovary,while the adaptive evolution of fertilization-related genes remains to be studied.In the present study,based on the genome and transcriptome information of black rockfish,a total of 10 hyaluronidase genes were identified by phylogenetic and sequence analyses,including hyal1,hyal2,hyal3,hyal4,hyal6 and spam1a,spam1b,spam1c and spam1d.The spam1 subfamilies,including spam1a,spam1b,spam1c and spam1d,were significantly expanded compared to other species.The adaptive evolution of hyaluronidase was further investigated by selection pressure analysis of branch model and branch site model.The results showed that only spam1 subfamily was positively selected with a large number of positive selection sites,and the evolution rate was significantly higher thanthose of other teleosts.Two positively selected sites,LYS-171 and GLY-164,were located in the neutral hyaluronidase activity domain,which was pivotal for SPAM1 to participate in enzymatic hydrolysis of the extracellular hyaluronic acid matrix and mediate acrosome reaction in mammals.Furthermore,spam1 was mainly expressed in spermatocytes,secondary spermatocytes,and spermatids of testis,whereas it was not found in metamorphic sperm and mature sperm based on the spatiotemporal expression analysis.All results indicated that spam1 might originate from the testis and might be an adaptation of viviparous trait in black rockfish.展开更多
A method of quantification of perfluorinated compounds(PFCs)from atmospheric particulate matter(APM)is described.A single step pretreatment method,selective pressurized liquid extraction(SPLE),was developed to reduce ...A method of quantification of perfluorinated compounds(PFCs)from atmospheric particulate matter(APM)is described.A single step pretreatment method,selective pressurized liquid extraction(SPLE),was developed to reduce the high matrix background and avoid contamination from commonly used multiple sample pretreatment steps.An effective sorbent was selected to purify the PFCs during SPLE,followed by liquid chromatography-tandem mass spectrometry(LC–MS/MS),for quantification of PFCs.Conditions affecting the SPLE efficiency,including temperature,static extraction time,and number of extraction cycles used,were studied.The optimum conditions were found to be 120℃,10 min,and 3 cycles,respectively.LC-MS/MS method was developed to obtain the optimal sensitivity specific to PFCs.The method detection limits(MDLs)were 0.006 to 0.48 ng/g for the PFCs studied and the linear response range was from 0.1 to 100 ng/g.To ensure accurate values were obtained,each step of the experiment was evaluated and controlled to prevent contamination.The optimized method was tested by performing spiking experiments in natural particulate matter matrices and good rates of recovery and reproducibility were obtained for all target compounds.Finally,the method was successfully used to measure 16 PFCs in the APM samples collected in Beijing over five years from 2015 to 2019.It is observed that some PFCs follow the trend of total PFC changes,and can be attributed to the environment influencing events and policy enforcement,while others don't seem to change as much with time of the year or from year to year.展开更多
[Objective]The aim of this study was to reveal the molecular evolutionary characteristics of dihydroflavonol 4-Reductase（DFR）—a key enzyme in anthocyanin synthesis pathway in Lamiidae plants.[Method]Based on DFR am...[Objective]The aim of this study was to reveal the molecular evolutionary characteristics of dihydroflavonol 4-Reductase（DFR）—a key enzyme in anthocyanin synthesis pathway in Lamiidae plants.[Method]Based on DFR amino acid and cDNA sequences released by NCBI,molecular evolution of DFR gene was analyzed with bioinformatic software.[Result]Seventeen plants fell into two major branches,Lamiidae and Liliidae.Most of the plants within a same family cluster assembled together,which basically accords with the morphological development of species.Prediction results based on selection pressure using MEGA,DNAsp and PAML software showed that DFR gene in Lamiidae plants underwent strong purifying selection pressure.[Conclusion]Our results laid basis for analyzing the molecular mechanism of enzymatic characteristics of DFR and of the anthocyanin synthesis pathway.展开更多
Mutants lacking wild-type MLO(Mildew resistance Locus O)proteins show broad-spectrum resistance to the powdery mildew fungus,and dysregulated cell death control,with spontaneous cell death in response to developmental...Mutants lacking wild-type MLO(Mildew resistance Locus O)proteins show broad-spectrum resistance to the powdery mildew fungus,and dysregulated cell death control,with spontaneous cell death in response to developmental or abiotic stimuli.In order to understand the evolution and divergence patterns of the MLO gene family in Rosaceae plants,we analysed systematically genome-wide data from Fragaria vesca,Prunus persica,Prunus mume,Malus domestica,Pyrus bretschneideri and Rubus occidentalis based on bioinformatics methods.Using three phylogenetic methods(the neighbour-joining,maximum likelihood,and Bayesian methods),we identified 117 MLO genes from 6 Rosaceae species.The results of all three phylogenetic analysis methods supported that these genes were divided into six clades.Conserved motif analysis found that only motif 2 was present in all MLO proteins and had 3 nearly invariant amino acid residues.The findings indicated that motif 2 might be shared by the MLO gene family.The structural features of these genes showed large variations in sequence length among different species,although the lengths and the numbers of exons exhibited high degrees of similarity.Selective pressure analysis showed extremely significant differences in all 6 clades,with 2,1,and 1 site(s)under significant positive selection detected in clades III,IV,and VI,respectively.These positive selection sites were important driving forces for the promotion of the functional differentiation of the MLO genes.Functional divergence analysis showed that the significantly divergent sites were located within the domains of the MLO genes.Functional distance analysis showed that the clade V had more conservative functions and might have retained more original functions during the evolutionary process.However,clade I may have undergone extensive altered functional constraints as a specialised functional role.Moreover,the most original function of the MLO genes in Rosaceae could be related to the evolution of their resistance to powdery mildew,which then gradually evolved into functions such as the regulation of flower development,the control of root morphology,and seed evolution due to the different evolutionary rates after gene duplication.These results provide a theoretical basis for further studies of the molecular evolutionary patterns of the plant MLO gene family.展开更多
DNA methylation is an important epigenetic regulation mechanism, which is catalyzed by DNA methyltransferases. In this study, eight DNA methyltransferase genes were identified in grape genome to analyze the selective ...DNA methylation is an important epigenetic regulation mechanism, which is catalyzed by DNA methyltransferases. In this study, eight DNA methyltransferase genes were identified in grape genome to analyze the selective pressure, gene expression and codon usage bias. The results showed grape DNA methyltransferase MET subfamily underwent relatively strong purifying selection during evolution, while chromomethylase CMT subfamily underwent positive selection during evolution. Under different abiotic(heat, drought or cold) stresses, the expression level of many grape DNA methyltransferase genes changed significantly. The expression level of these genes might be related with cis-regulatory elements of their promoters. The results of codon usage bias analysis showed that synonymous codon bias existed in grape DNA methyltransferase gene family, which might be affected by mutation pressure. These results laid a solid foundation for in-depth study of DNA methyltransferases in grape.展开更多
Limb reduction in Squamata present the dramatic characteristic to focus and usually accompanied with particularly morphological modifications, impacting tremendous locomotion changing and might generate different ener...Limb reduction in Squamata present the dramatic characteristic to focus and usually accompanied with particularly morphological modifications, impacting tremendous locomotion changing and might generate different energy requirement. Herein, we combined both morphological and mitochondrial genomic data to explore the evolution of phenotypic transformation and mitochondrial genome of limbless and body-elongated squamates. We collected phenotypic measurements of 503 individuals, representing limbed or limbless taxa across all major lineages in Squama ta to investiga te the morphological correla tions with limb-reduction. Furthermore, we provided the mitochondrial genome of the representative limbless and elongated species Dibamus bourreti(Angel, 1935) to detect selective constraints on limbless clades with published mitogenomes of other squa ma te reptiles. Our results evidenced tha t body elongation had certain negative relationship with limbreduction in Squamata lineage and Lacertilia lineage(R = –0.495, P < 2.2 e-16;R= –0.332, P = 1.1 e-13, respectively), while tail length showed slight correlation in both clades(R = 0.156, P = 4.3 e-04;R= 0.192, P = 2.1 e-05, respectively). Besides, detection demonstrated that ATP6 has experienced accelerated evolution among limbless lineages, suggesting selective pressure on mitogenomes may play an essential role in energy disparity for locomotion of limbed and limbless squamates.展开更多
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
In order to reduce the pressure of parameter selection and avoid trapping into the local optimum,a novel differential evolution( DE) algorithm without crossover rate is proposed. Through embedding cellular automata in...In order to reduce the pressure of parameter selection and avoid trapping into the local optimum,a novel differential evolution( DE) algorithm without crossover rate is proposed. Through embedding cellular automata into the DE algorithm,those interactions among vectors are restricted within cellular structure of neighbors while the cell own evolution,which may be used to balance the tradeoff between exploration and exploitation and then tune the selection pressure. And further more,the orthogonal crossover without crossover rate is used instead of the binomial crossover,which can maintain the population diversity and accelerate the convergence rate. Experimental studies are carried out on a suite of 7 bound-constrained numerical benchmark functions. The results show that the proposed algorithm has better capability of maintaining the population diversity and faster convergence than the classical differential evolution and several classic differential evolution variants.展开更多
基金supported by the National Natural Science Foundation of China(32160254)Yunnan Fundamental Research Projects(202401AS070039).
文摘Background:A thorough examination of the physicochemical properties,higher-order structure,subcellular localization,and selective pressure of the cytochrome c oxidase subunit I(COX1)protein of the endemic species Eothenomys miletus(E.miletus)in the Hengduan Mountains provides further insights into molecular characteristics and function of the COX1 gene in E.miletus.Method:The physicochemical properties and higher-order structure of the COX1 protein of E.miletus were analyzed using bioinformatics software.Subsequently,a phylogenetic tree was constructed using Mega 7.0 software based on the COX1 gene from 19 species of the Arvicolinae subfamily and 3 species of the Muridae.Selection pressure analysis was performed using the PAML 4.7 software and the Datamonkey online website.Results:The COX1 protein of E.miletus comprises/consists of 514 amino acids,with leucine(Leu/L)being the most prevalent amino acid(11.5%).This hydrophilic protein contains 42 phosphorylation sites and 4 N-glycosylation sites.It possesses a transmembrane domain and lacks signal peptide distribution,thus classifying it as a non-GPI-anchored protein.The secondary structure of the COX1 protein consists ofα-helices(36.77%),random coils(33.85%),and extended chains,a composition consistent with/findings that align with its tertiary structure.Significant genetic differentiation exists among species within the Arvicolinae subfamily,a finding consistent with morphological identification results.The COX1 gene in Arvicolinae species exhibits purifying selection.Conclusion:This study analyzed the physicochemical properties of the COX1 protein in E.miletus.Phylogenetic and selection pressure analyses reveal significant genetic divergence among Arvicolinae species,and demonstrate that the COX1 gene is evolutionarily conserved within the Arvicolinae subfamily.
基金Supported by Natural Science Foundation of Jiangsu Province(BK2009235)~~
文摘[Objective]The aim was to research the relationship between nucleotide substitutions rate and selective pressure.[Method]Synonymous and nonsynonymous substitutions and their ratios for some sorghum and maize genes in nucleus and organelle genomes were analyzed by statistical method,and comparative analysis of related functional genes were carried out.[Result]The pure selective pressures of the related functional genes were similar between nucleus and chloroplast genomes,but was lower in mitochondrial genome.The significant differences of nucleotide substitution rate between sorghum and maize orthologous genes in nucleus genome,and among different functional genes in nucleus genome were mainly due to the nonsynonymous substitution difference.[Conclusion]The molecular evolutional rate of different functional genes and different lineages were influenced by selective pressure.The differences of molecular evolutional rate among nucleus,chloroplast and mitochondria genomes had no direct relationship with selective pressure.
基金supported by the National Natural Science Foundation of China (No. 51208231)
文摘A novel method based on the selective pressure of particle size （particle-size cultivation method, PSCM） was developed for the cultivation and operation of aerobic granular sludge in a continuous-flow reactor, and compared with the conventional method based on the selective pressure of settling velocity （settling-velocity cultivation method, SVCM）. Results indicated that aerobic granules could be cultivated in continuous operation mode by this developed method within 14 days. Although in the granulation process, under particle-size selective pressure, mixed liquor suspended solids （MLSS） in the reactor fluctuated greatly and filamentous bacteria dominated the sludge system during the initial operation days, no obvious difference in profile was found between the aerobic granules cultivated by PSCM and SVCM. Moreover, aerobic granules cultivated by PSCM presented larger diameter, lower water content and higher specific rates of nitrification, denitrifieation and phosphorus removal, but lower settling velocity. Under long term operation of more than 30 days, aerobic granules in the continuous-flow reactor could remain stable and obtain good chemical oxygen demand （COD）, NH4^＋-N, total nitrogen （TN） and total phosphorus （TP） removal. The results indicate that PSCM was dependent on the cultivation and maintenance of the stability of aerobic granules in continuous-flow bioreactors.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDA19050302)the National Natural Science Foundation of China(Grant Nos.31871328 and 32030021)+1 种基金the National Key R&D Program of China(Grant No.2017YFC0907502)the International Partnership Program of the Chinese Academy of Sciences(Grant No.153F11KYSB20160008).
文摘KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences.Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences,selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences.As testified on empirical data,KaKs_Calculator 3.0 shows effectiveness to detect the strength and mode of selection operated on molecular sequences,accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at a whole-genome scale.The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.
文摘To study the quasispecies diversity of porcine reproductive and respiratory syndrome virus (PRRSV), open reading frame 5 (ORF5) of strain SD0612 was amplified and cloned. Sixty clones of ORF5 were sequenced and analyzed with DNAStar software. Nucleic acid sequence homology was 97.7%-100%, with 78 mutations observed. Among these 60 clones, the sequences of 17 clones were identical and recognized as the dominant quasispecies of strain SD0612. Evolution of SD0612 quasispecies diversity under antibody selective pressure was also studied. SD0612 was passed continuously in the Marc-145 cell line over 40 passages in 6 independent lineages. SD0612 antiserum was not added to lineage A, B, and C cultures; however, antiserum was added to culture medium for lineages D, E, and F. PRRSV ORF5 was then amplified, cloned, and sequenced from each of the 6 lineages, designated as A40-F40. F40 was further passed in Marc-145 cells using 6 independent lineages with or without F40 antiserum for another 40 passages. ORF5 from the 6 newly-derived virus lineages, which we designated as a40-f40, were amplified, cloned and sequenced. The proportion of dominant quasispecies increased with passage number in cell cultures supplemented with antibodies, but decreased when antibodies were lacking. Our work has demonstrated a diversity of quasispecies for ORF5 in PRRSV SD0612. Antibody selective pressure was able to significantly influence quasispecies diversity and promote a dominant quasispecies that was able to evade immune reactions.
基金supported by the“Pioneer”and“Leading Goose”R&D Program of Zhejiang(No.2022C04014)Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding(No.2021C02068-10).
文摘Birds,a fascinating and diverse group occupying various habitats worldwide,exhibit a wide range of life-history traits,reproductive methods,and migratory behaviors,all of which influence their immune systems.The association between major histocompatibility complex(MHC)genes and certain ecological factors in response to pathogen selection has been extensively studied;however,the role of the co-working molecule T cell receptor(TCR)remains poorly understood.This study aimed to analyze the copy numbers of TCR-V genes,the selection pressure(ωvalue)on MHC genes using available genomic data,and their potential ecological correlates across 93 species from 13 orders.The study was conducted using the publicly available genome data of birds.Our findings suggested that phylogeny influences the variability in TCR-V gene copy numbers and MHC selection pressure.The phylogenetic generalized least squares regression model revealed that TCR-Vαδcopy number and MHC-I selection pressure were positively associated with body mass.Clutch size was correlated with MHC selection pressure,and Migration was correlated with TCR-Vβcopy number.Further analyses revealed that the TCR-Vβcopy number was positively correlated with MHC-IIB selection pressure,while the TCR-Vγcopy number was negatively correlated with MHC-I peptide-binding region selection pressure.Our findings suggest that TCR-V diversity is significant in adaptive evolution and is related to species’life-history strategies and immunological defenses and provide valuable insights into the mechanisms underlying TCR-V gene duplication and MHC selection in avian species.
基金supported by the National Natural Science Foundation of China(32270670,32288101,32271186,and 32200482)the National Basic Research Program of China(2015FY111700)the CAMS Innovation Fund for Medical Sciences(2019-I2M-5-066).
文摘Mitochondria play a key role in lipid metabolism,and mitochondrial DNA(mtDNA)mutations are thus considered to affect obesity susceptibility by altering oxidative phosphorylation and mitochondrial function.In this study,we investigate mtDNA variants that may affect obesity risk in 2877 Han Chinese individuals from 3 independent populations.The association analysis of 16 basal mtDNA haplogroups with body mass index,waist circumference,and waist-to-hip ratio reveals that only haplogroup M7 is significantly negatively correlated with all three adiposity-related anthropometric traits in the overall cohort,verified by the analysis of a single population,i.e.,the Zhengzhou population.Furthermore,subhaplogroup analysis suggests that M7b1a1 is the most likely haplogroup associated with a decreased obesity risk,and the variation T12811C(causing Y159H in ND5)harbored in M7b1a1 may be the most likely candidate for altering the mitochondrial function.Specifically,we find that proportionally more nonsynonymous mutations accumulate in M7b1a1 carriers,indicating that M7b1a1 is either under positive selection or subject to a relaxation of selective constraints.We also find that nuclear variants,especially in DACT2 and PIEZO1,may functionally interact with M7b1a1.
基金Funding Statement:This work was funded by the National Natural Science Foundation of China(32100132)Shandong Province Natural Sciences Foundation of China(ZR2021QC008)+1 种基金Youth Innovation Team Program'in College of Shandong Province of China(2022KJ119)supported by Young Talent of Lifting Engineering for Science and Technology in Shandong,China(SDAST2024QT085).
文摘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.
基金supported by the National Natural Science Foundation of China(21732002,22077043,31672558,31871305,21907036)Opening Foundation of State Key Laboratory of Freshwater Ecology and Biotechnology,China(2020FB08)+2 种基金the Fundamental Research Funds for the(2662018PY021,2662019PY003,2662020PY001)Huazhong Agricultural University Scientific&Technological Self-innovation Foundation(2016RC011)HZAU-AGIS Cooperation Fund(SZYJY2021010)。
文摘G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world is the result of natural selection for functionality. In this study, we identified putative quadruplex-forming sequences(PQSs) across the known viral genomes and analyzed the abundance, structural stability, and conservation of viral PQSs. A Viral Putative G-quadruplex Database(http://jsjds.hzau.edu.cn/MBPC/Vi PGD/index.php/home/index) was constructed to collect the details of each viral PQS, which provides guidance for selecting the desirable PQS. The PQS with two putative G-tetrads(G2-PQS) was significantly enriched in both eukaryotic viruses and prokaryotic viruses, whereas the PQSs with three putative G-tetrads(G3-PQS) were only enriched in eukaryotic viruses and depleted in prokaryotic viruses. The structural stability of PQSs in prokaryotic viruses was significantly lower than that in eukaryotic viruses. Conservation analysis showed that the G2-PQS, instead of G3-PQS, was highly conserved within the genus. This suggested that the G2-quadruplex might play an important role in viral biology, and the difference in the occurrence of G-quadruplex between eukaryotic viruses and prokaryotic viruses may result from the different selection pressures from hosts.
文摘Positive selection and differential selective pressure analyses were carried out to study Haemagglutinin (HA) genes of H9N2 influenza viruses from different hosts in this paper. Results showed that, although most positions in HAs were under neutral or purifying evolution, a few positions located in the antigenic regions and receptor binding sites were subject to positive selection and some of them were even positively selected at the population level. In addition, there were always some positions differentially selected for viruses from different hosts. Both selection pressure working on HA codons and positions differentially selected might account for the extension of the host range and adaptations to different hosts of H9N2 influenza viruses.
文摘AIM： To evaluate the efficacy of selective laser trabeculoplasty（SLT） in glaucomatous eyes with previous incisional glaucoma surgery. METHODS： A retrospective cohort of eyes that underwent SLT at a single institution from 2013-2015 were followed for 1 y. Reduction in intraocular pressure（IOP） following SLT was evaluated in eyes with prior trabeculectomy with Ex Press mini shunt（Alcon, Ft Worth, TX, USA）, Ahmed valve（New World Medical, Cucamonga, CA, USA）, or combined phacoemulsification-trabeculectomy. A control group was included with eyes without prior surgery that underwent SLT. Success was defined as 〉20% drop in IOP from pre-SLT baseline. RESULTS： One-hundred and six eyes were included with 53 in both the prior glaucoma surgery（PGS） and no prior glaucoma surgery（NPGS） groups. Mean pre-SLT IOP was 19.2±4.3 and 20.6±6.0 mm Hg for PGS and NPGS groups, respectively（P=0.17）. Both groups produced statistically significant IOP reductions at 1 and 6 mo（P〈0.04）. At 6 mo, mean IOP reduction reached 7.3% and 10.8% for the PGS and NPGS groups, respectively（P=0.42）. Overall, 27.9% and 31.7% of eyes in PGS and NPGS groups met success criteria at 1 y（P=0.70）. In the PGS group, eyes with baseline IOP ≥21 mm Hg had IOP reductions of 18.1%（P〈0.001）, 16.7%（P〈0.01）, and 8.4%（P=0.31） compared to eyes with baseline IOP 〈21 mm Hg who had IOP reductions of 2.3%（P=0.39）, 3.4%（P=0.19）, and 1.1%（P=0.72） at 1, 6 mo, and 1 y, respectively. CONCLUSION： SLT is efficacious in eyes with prior incisional glaucoma surgery and results in similar IOP reductions compared to eyes without PGS. A larger IOP reduction is observed following SLT in eyes with higher pre-SLT IOP.
基金supported by the National Natural Science Foundation of China(Nos.32273133,31970492).
文摘Black rockfish(Sebastes schlegelii)has evolved viviparous reproduction mode.Different from the oviparous fishes,the spermatozoa of black rockfish are stored on the surface of ovarian follicle for over four months until the egg mature in ovary,while the adaptive evolution of fertilization-related genes remains to be studied.In the present study,based on the genome and transcriptome information of black rockfish,a total of 10 hyaluronidase genes were identified by phylogenetic and sequence analyses,including hyal1,hyal2,hyal3,hyal4,hyal6 and spam1a,spam1b,spam1c and spam1d.The spam1 subfamilies,including spam1a,spam1b,spam1c and spam1d,were significantly expanded compared to other species.The adaptive evolution of hyaluronidase was further investigated by selection pressure analysis of branch model and branch site model.The results showed that only spam1 subfamily was positively selected with a large number of positive selection sites,and the evolution rate was significantly higher thanthose of other teleosts.Two positively selected sites,LYS-171 and GLY-164,were located in the neutral hyaluronidase activity domain,which was pivotal for SPAM1 to participate in enzymatic hydrolysis of the extracellular hyaluronic acid matrix and mediate acrosome reaction in mammals.Furthermore,spam1 was mainly expressed in spermatocytes,secondary spermatocytes,and spermatids of testis,whereas it was not found in metamorphic sperm and mature sperm based on the spatiotemporal expression analysis.All results indicated that spam1 might originate from the testis and might be an adaptation of viviparous trait in black rockfish.
基金supported by the NQI Project of National key R&D Program of China (No.2016YFF0201102)the project for the“Development of analytical method and certified reference materials for tracing air pollutant source” (No.21AKY1514)from the National Institute of Metrology,Beijing,China。
文摘A method of quantification of perfluorinated compounds(PFCs)from atmospheric particulate matter(APM)is described.A single step pretreatment method,selective pressurized liquid extraction(SPLE),was developed to reduce the high matrix background and avoid contamination from commonly used multiple sample pretreatment steps.An effective sorbent was selected to purify the PFCs during SPLE,followed by liquid chromatography-tandem mass spectrometry(LC–MS/MS),for quantification of PFCs.Conditions affecting the SPLE efficiency,including temperature,static extraction time,and number of extraction cycles used,were studied.The optimum conditions were found to be 120℃,10 min,and 3 cycles,respectively.LC-MS/MS method was developed to obtain the optimal sensitivity specific to PFCs.The method detection limits(MDLs)were 0.006 to 0.48 ng/g for the PFCs studied and the linear response range was from 0.1 to 100 ng/g.To ensure accurate values were obtained,each step of the experiment was evaluated and controlled to prevent contamination.The optimized method was tested by performing spiking experiments in natural particulate matter matrices and good rates of recovery and reproducibility were obtained for all target compounds.Finally,the method was successfully used to measure 16 PFCs in the APM samples collected in Beijing over five years from 2015 to 2019.It is observed that some PFCs follow the trend of total PFC changes,and can be attributed to the environment influencing events and policy enforcement,while others don't seem to change as much with time of the year or from year to year.
基金Supported by the Fundamental Research Funds for the Central Universities(SWJTU09BR208)~~
文摘[Objective]The aim of this study was to reveal the molecular evolutionary characteristics of dihydroflavonol 4-Reductase（DFR）—a key enzyme in anthocyanin synthesis pathway in Lamiidae plants.[Method]Based on DFR amino acid and cDNA sequences released by NCBI,molecular evolution of DFR gene was analyzed with bioinformatic software.[Result]Seventeen plants fell into two major branches,Lamiidae and Liliidae.Most of the plants within a same family cluster assembled together,which basically accords with the morphological development of species.Prediction results based on selection pressure using MEGA,DNAsp and PAML software showed that DFR gene in Lamiidae plants underwent strong purifying selection pressure.[Conclusion]Our results laid basis for analyzing the molecular mechanism of enzymatic characteristics of DFR and of the anthocyanin synthesis pathway.
基金supported by the National Key R&D Program of China(Grant No.2018YFD1000400)National Natural Science Foundation of China(Grant Nos.31860571 and 31560565)+1 种基金Major Science and Technology Projects Yunnan Province(Grant No.2016ZA005)Yunnan Youth Academic&Technical Leaders Reserve Talents Training Project(Grant No.2015HB078)。
文摘Mutants lacking wild-type MLO(Mildew resistance Locus O)proteins show broad-spectrum resistance to the powdery mildew fungus,and dysregulated cell death control,with spontaneous cell death in response to developmental or abiotic stimuli.In order to understand the evolution and divergence patterns of the MLO gene family in Rosaceae plants,we analysed systematically genome-wide data from Fragaria vesca,Prunus persica,Prunus mume,Malus domestica,Pyrus bretschneideri and Rubus occidentalis based on bioinformatics methods.Using three phylogenetic methods(the neighbour-joining,maximum likelihood,and Bayesian methods),we identified 117 MLO genes from 6 Rosaceae species.The results of all three phylogenetic analysis methods supported that these genes were divided into six clades.Conserved motif analysis found that only motif 2 was present in all MLO proteins and had 3 nearly invariant amino acid residues.The findings indicated that motif 2 might be shared by the MLO gene family.The structural features of these genes showed large variations in sequence length among different species,although the lengths and the numbers of exons exhibited high degrees of similarity.Selective pressure analysis showed extremely significant differences in all 6 clades,with 2,1,and 1 site(s)under significant positive selection detected in clades III,IV,and VI,respectively.These positive selection sites were important driving forces for the promotion of the functional differentiation of the MLO genes.Functional divergence analysis showed that the significantly divergent sites were located within the domains of the MLO genes.Functional distance analysis showed that the clade V had more conservative functions and might have retained more original functions during the evolutionary process.However,clade I may have undergone extensive altered functional constraints as a specialised functional role.Moreover,the most original function of the MLO genes in Rosaceae could be related to the evolution of their resistance to powdery mildew,which then gradually evolved into functions such as the regulation of flower development,the control of root morphology,and seed evolution due to the different evolutionary rates after gene duplication.These results provide a theoretical basis for further studies of the molecular evolutionary patterns of the plant MLO gene family.
基金Supported by Major Agricultural Application Technology Innovation Project of Shandong Province"Research and Application of Precision Control of Maturation and Product Innovation of Featured Brewing Grape"Major Agricultural Application Technology Innovation Project of Shandong Province"Development of Landmark Wines and Integrated Application of Key Technologies in Shandong Province"Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences(CXGC2016D01)
文摘DNA methylation is an important epigenetic regulation mechanism, which is catalyzed by DNA methyltransferases. In this study, eight DNA methyltransferase genes were identified in grape genome to analyze the selective pressure, gene expression and codon usage bias. The results showed grape DNA methyltransferase MET subfamily underwent relatively strong purifying selection during evolution, while chromomethylase CMT subfamily underwent positive selection during evolution. Under different abiotic(heat, drought or cold) stresses, the expression level of many grape DNA methyltransferase genes changed significantly. The expression level of these genes might be related with cis-regulatory elements of their promoters. The results of codon usage bias analysis showed that synonymous codon bias existed in grape DNA methyltransferase gene family, which might be affected by mutation pressure. These results laid a solid foundation for in-depth study of DNA methyltransferases in grape.
基金supported by the National Natural Science Foundation of China (31772434,32070410)the Second Tibetan Plateau Scientific Expedition a nd Resea rch Progra m(STEP) (2019QZKK0501)+2 种基金the International Partnership Program of Chinese Academy of Sciences (151751KYSB20190024)Biological Resources Programme, Chinese Academy of Sciences (KF JBRP-017-14)the Distinguished young scholars in Sichuan Province (2021JDJQ0002)。
文摘Limb reduction in Squamata present the dramatic characteristic to focus and usually accompanied with particularly morphological modifications, impacting tremendous locomotion changing and might generate different energy requirement. Herein, we combined both morphological and mitochondrial genomic data to explore the evolution of phenotypic transformation and mitochondrial genome of limbless and body-elongated squamates. We collected phenotypic measurements of 503 individuals, representing limbed or limbless taxa across all major lineages in Squama ta to investiga te the morphological correla tions with limb-reduction. Furthermore, we provided the mitochondrial genome of the representative limbless and elongated species Dibamus bourreti(Angel, 1935) to detect selective constraints on limbless clades with published mitogenomes of other squa ma te reptiles. Our results evidenced tha t body elongation had certain negative relationship with limbreduction in Squamata lineage and Lacertilia lineage(R = –0.495, P < 2.2 e-16;R= –0.332, P = 1.1 e-13, respectively), while tail length showed slight correlation in both clades(R = 0.156, P = 4.3 e-04;R= 0.192, P = 2.1 e-05, respectively). Besides, detection demonstrated that ATP6 has experienced accelerated evolution among limbless lineages, suggesting selective pressure on mitogenomes may play an essential role in energy disparity for locomotion of limbed and limbless squamates.
基金supported by the National Natural Science Foundation of China(No.11701546).
文摘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.
基金Supported by the National Natural Science Foundation of China(No.61501186)the Jiangxi Province Science Foundation(No.20171BAB202001)the Visiting Scholar Foundation of Jiangxi Province Young and Middle-aged University Teachers'Development Program([2016],No.169)
文摘In order to reduce the pressure of parameter selection and avoid trapping into the local optimum,a novel differential evolution( DE) algorithm without crossover rate is proposed. Through embedding cellular automata into the DE algorithm,those interactions among vectors are restricted within cellular structure of neighbors while the cell own evolution,which may be used to balance the tradeoff between exploration and exploitation and then tune the selection pressure. And further more,the orthogonal crossover without crossover rate is used instead of the binomial crossover,which can maintain the population diversity and accelerate the convergence rate. Experimental studies are carried out on a suite of 7 bound-constrained numerical benchmark functions. The results show that the proposed algorithm has better capability of maintaining the population diversity and faster convergence than the classical differential evolution and several classic differential evolution variants.
