Analysis on the Relationship between Selective Pressure and Nucleotide Substitution Rate in Nucleus and Organelle Genes of Sorghum and Maize

[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.

KaKs_Calculator 3.0:Calculating Selective Pressure on Coding and Non-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.

Evolution of quasispecies diversity for porcine reproductive and respiratory syndrome virus under antibody selective pressure

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.

Aerobic granules cultivated and operated in continuous-flow bioreactor under particle-size selective pressure

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.

Genome-Wide Characterization of the Hyaluronidase Gene Family and Their Potential Roles in Viviparous Black Rockfish(Sebastes schlegeli)

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.

Selection Pressure on Haemagglutinin Genes of H9N2 Influenza Viruses from Different Hosts

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.

Efficacy of selective laser trabeculoplasty following incisional glaucoma surgery

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.

Genomic Landscape of Rare Codon Usage at Start Region in the Pacific Oyster Genome

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.

Molecular Evolutionary Analysis of DFR Gene in Lamiidae Plants

[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.

Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

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.

Genome-wide Identification and Analysis of DNA Methyltransferases in Grape

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.

Evolution of Phenotype and Mitochondrial Genome Reveals Limbless and Body-elongated Squamates may Change Their Energy Basis for Locomotion

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.

Novel differential evolution algorithm with spatial evolution rules

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.

Positive Selection Analysis of VP1 Genes of Worldwide Human Enterovirus 71 Viruses

Human enterovirus 71 viruses have been long circulating throughout the world. In this study, we performed a positive selection analysis of the VP1 genes of capsid proteins from Enterovirus 71 viruses. Our results showed that although most sites were under negative or neutral evolution, four positions of the VP1 genes were under positive selection pressure. This might account for the spread and frequent outbreaks of the viruses and the enhanced neurovirulence. In particular, position 98 might be involved in neutralizing antibodies, modulating the virus-receptor interaction and enhancing the virulence of the viruses. Moreover, both positions 145 and 241 might correlate to determine the receptor specificity. However, these positions did not display much difference in amino acid polymorphism. In addition, no position in the VP1 genes of viruses isolated from China was under positive selection.

Correlation between Climatic Factors and Genetic Diversity of Phrynocephalus forsythii

Global climate change is a threat to animals in nearly all biomes and ecosystems, especially for ectotherm whose life activities highly depend on environmental thermal regime. Population genetic diversity which is essential for adaptation to environmental change is a useful index for long-term species survival. In this paper, genetic diversity of eight Phrynocephalus forsythii population which distributed in Tarim Basin, China, were evaluated based on three mtDNA gene and its correlation with environment factors were investigated using RDA. Our result revealed that, the level of genetic diversity of P. forsythii populations was related to its location but there was no significant correlation between genetic distances and geographic distances in P. forsythii. However, we find that mtDNA of P. forsythii was subjected to selection pressure during evolution and population genetic diversity was significantly positively related to variation coefficient of rainfall(VCR) and altitude(AL), while significantly negatively related to longitude(N) and annual average temperature(AAT). Our result supported the previous prediction that excessive ambient heat is a threat to P. forsythii.

Hybrid Multipopulation Cellular Genetic Algorithm and Its Performance

The selection pressure of genetic algorithm reveals the degree of balance between the global exploration and local optimization.A novel algorithm called the hybrid multi-population cellular genetic algorithm(HCGA)is proposed,which combines population segmentation with particle swarm optimization(PSO).The control parameters are the number of individuals in the population and the number of subpopulations.By varying these control parameters,changes in selection pressure can be investigated.Population division is found to reduce the selection pressure.In particular,low selection pressure emerges in small and highly divided populations.Besides,slight or mild selection pressure reduces the convergence speed,and thus a new mutation operator accelerates the system.HPCGA is tested in the optimization of four typical functions and the results are compared with those of the conventional cellular genetic algorithm.HPCGA is found to significantly improve global convergence rate,convergence speed and stability.Population diversity is also investigated by HPCGA.Appropriate numbers of subpopulations not only achieve a better tradeoff between global exploration and local exploitation,but also greatly improve the optimization performance of HPCGA.It is concluded that HPCGA can elucidate the scientific basis for selecting the efficient numbers of subpopulations.

Isolation and phylogenetic analysis of feline calicivirus strains from various region of China

Feline calicivirus(FCV)is an important feline pathogen mainly causing upper respiratory tract disease,conjunctivitis,and stomatitis,and it is classifed into genotype I and genotype II.To investigate the prevalence and molecular characteristics of FCV,this study collected 337 cat swab samples from animal hospitals in diferent regions of China from 2019 to 2021.The positive detection rate of FCV was 29.9%(101/337)by RT-PCR.Statistical analysis showed that FCV prevalence was signifcantly associated with living environment(p=0.0004),age(p=0.031)and clinical symptoms(p=0.00),but not with sex(p=0.092)and breed(p=0.171).The 26 strains of FCV were isolated using F81 cells.Phylogenetic analysis showed that 10 isolates belonged to genotype I,and 16 isolates belonged to genotype II.These 26 isolates were highly genetically diverse,of which HB7 isolate had three same virulence-related amino acid loci with VSD strains.Potential loci distinguishing diferent genotypes were identifed from 26 isolates,suggesting the genetic relationship between diferent genotypes.In addition,selection pressure analysis based on capsid protein of 26 isolates revealed that the protein is under diversifying selection.This study reveals the genetic diversity of FCV and provides a reference for the screening of vaccine candidate strains and the development of vaccines with better cross-protection efects.

Differential selection in HIV-1 gp120 between subtype B and East Asian variant B'

HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world.For instance,distinct genomic backgrounds can be observed between the pandemic subtype B,prevalent in Europe and North-America,and its offspring clade B＇ in East Asia.Here we ask whether this differentiation affects the selection pressure experienced by the virus.To answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120 at the level of individual codons using a simple and fast estimation method based on the ratio ka/ks of amino acid changes to synonymous changes.To validate the approach we compare results to those from a state-of-the-art mixed-effect method.The agreement is acceptable,but the analysis also demonstrates some limitations of the simpler approach.Further,we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B＇ with more directional selection pressure in variable loops and more stabilizing selection in the constant regions.Focusing on codons with increased ka/ks values in B＇,we show that these codons are scattered over the whole of gp120,with remarkable clusters of higher density in regions flanking the variable loops.We identify a significant statistical association of glycosylation sites and codons with increased ka/ks values.

Functional structure analysis and genome‑wide identification of CNX gene family in cotton

Background:Under abiotic stress conditions,cotton growth is inhibited and yield losses are severe.Identification of calnexin family members and function analysis under abiotic stress laid the foundation for the screening of stressrelated candidate genes.Results:A total of 60 CNX family members have been identified in Gossypium hirsutum,G.barbadense,G.arboreum,and G.raimondii,and they were divided into two categories:CNX and CRT genes.Through the construction of a phylogenetic tree,they were subdivided into three classes.Further analysis of chromosome localization,conserved promoters,gene structure and selection under pressure showed that the family members were highly conserved in the evolution process.Analysis of cis-acting elements in the promoter regions showed that CNX family genes contain regulatory elements for growth and development,anaerobic,drought,defense and stress response,and plant hormones.Using RNA-seq data to study the expression pattern of GhCNX genes under cold,hot,salt stress and Polyethylene glycol,it was observed that the gene expression levels changed by different degrees under different stress conditions,indicating that GhCNX members were involved in the regulation of multiple biological stresses.Conclusion:This study provides an insight into the members of cotton CNX genes.The results of this study suggested that CNX family members play a role in defense against adversity and provide a foundation for the discovery of stress-related genes.

Complete Genome Sequence Analysis of Guangdong Isolates of Cymbidium Mosaic Virus

[Objectives]The paper was to explore the genetic information and evolution of CymMV,and to provide an important scientific basis for monitoring and early warning of orchid virus disease and anti-virus genetic engineering of orchid in Guangdong Province.[Methods]RT-PCR and DASELISA were used to detect and identify CymMV from leaves with suspected virus disease of Cymbidium sinense collected from Guangzhou area.The genome sequence assembly,annotation,phylogeny and selection pressure analysis of CymMV isolates were performed with related molecular biology software.[Results]Two CymMV isolates(GZV013 and ZC29)were found in Guangdong Province for the first time in this study.The genome of both GZV013 and ZC29 were 6227 nt in length,encoding 5 functional proteins.The similarity analysis of the full sequence showed that the nucleotide sequence identity of GZV013 and Taiwan isolate M2 was 97.03% and that of ZC29 and Nanjing isolate NJ-1 was 97.11%.The complete genome sequence identity among CymMV isolates ranged from 86.85% to 98.31%,and the differentiation of diverse populations was closely related to host species and geographical isolation.Each region of CymMV genome was affected by negative selection and conformed to the neutral evolution model.The genes encoding RdRp,TGB1 and TGB2 had the highest mutation rates in the genome.[Conclusions]GZV013 was most closely related to Taiwan isolate M2,and ZC29 was most closely related to Nanjing isolate NJ-1,belonging to the same branch of a family.