Analysis of Genetic Evolution of Escherichia fergusonii

[Objectives]This study was conducted to explore the genetic evolution of Escherichia fergusonii in different countries and regions,and to clarify the genetic relationship of E.fergusonii in different countries and regions.[Methods]Bioinformatics method and bacterial 16 S rRNA sequencing technology were used to sort out and prune 16 S rRNA genes isolated in laboratory and searched in NCBI database to construct a molecular evolutionary tree for analysis and comparison.[Results]The direction of evolution of E.fergusonii has broken through regions,and there was cross evolution among continents.The origin of E.fergusonii was the Asian continent,and its adaptability to arid climate was not strong.[Conclusions]This study revealed the genetic evolution laws of E.fergusonii in the spread and mutation of livestock and poultry diseases,and provides a theoretical reference for the prevention and treatment of the disease.

Identification and Antibacterial Activity Study of a Terrestrial Strain of Brevibacterium aureus 431

This study isolated and purified strain 431 from an animal probiotic product.Through staining and microscopic examination,colony morphology analysis,biochemical reaction tests,and 16S rDNA sequence alignment,the strain was identified and named Brevibacterium aureus 431.The study focused on the production of biosurfactants by strain 431,and antibacterial activity tests were conducted on the strain and its secondary metabolites.The results showed that strain 431 exhibited no resistance to 10 commonly used drugs,and its concentrated secondary metabolites were highly sensitive to the indicator bacterium Escherichia coli.Oral administration of strain 431 to BALB/c mice resulted in normal mental state,diet,and bowel movements,with no signs of illness or death,indicating that strain 431 is highly safe and non-pathogenic to mice.The study suggests that Brevibacterium aureus 431 has significant research value as a new source of actinomycetes and that its secondary metabolites have potential application value in the development of antibacterial drugs.

Analysis of Genetic Polymorphic SSR Markers in Germplasm Resources of the Natural Colored Cotton

Short sequence repeats(microsatellite,SSR) and expressed sequence tags-SSR(EST-SSR) markers were employed to analyze the genetic diversity of natural colored cotton varieties.About

Polyploidization Genetic Mechanism of Sugarcane Genome

The sugarcane genome polyploidization can reduce the pressure of gene evolution selection,promote the fixation of fine traits,and increase the biomass and economic value of sugarcane.This paper mainly introduced the origin of the sugarcane genome,the chromosome composition,the research progress of polyploidization genetic mechanism,in the hope of providing theoretical reference for sugarcane polyploidization breeding.

Genetic Advances in Genome and Phenotypic Characters of Domestic Dog

Dogs represent such a rich potential resource to further understand diseases and genetic traits.Comparing the genomes of three species of canine,human,and rat in terms of genome analysis,it is found that dogs are highly conservative with humans and rats.The special population structure of dogs makes it a good model for studying the diversity of morphology and behavior,the genetic basis of mammalian evolution,and dis-eases.This article gives a brief review of recent advances in domestic dog origin and evolution,genomic structure,genetic variation in dog pheno-typic characteristics,and gene mapping.These research results are expected to provide a better theoretical basis for canine genetic breeding re-search and provide new ideas and methods for the prevention,diagnosis and treatment of human diseases.

Genetic Characteristics of <i>Citrus Tristeza Virus</i>Isolates from Cultivated Citrus in China Based on Coat Protein Gene

Citrus tristeza virus (CTV) is an important citrus pathogen causing considerable economic loss to citrus production. Knowledge on genetic evolutionary of the CTV population in China remains limited. In this study, 1439 samples were collected from nine citrus-producing areas of China. The coat protein (CP) genes of CTV were amplified by RT-PCR, and sequenced to analyze the genetic evolution. Analysis of the base composition showed an AU preference pattern, with the GC content was lower than AU content. Nine CTV populations were clustered into one clade in neighbor-joining (NJ) tree, indicative of a close phylogenetic relationship among the populations in China. Analysis of molecular variation (AMOVA) revealed that 77.72% genetic variations of CTV populations were observed among populations, with an FST value of 0.223. The values of dN/dS and neutrality test of CP gene were ranged from 0.016 to 0.082 and -1.377 to 1.456, respectively, the results suggesting that all of nine CTV populations were relatively constantly maintained under purifying selection. Our study demonstrated the genetic characteristics and molecular evolution relationship of CTV populations in China, and provided a theoretical basis for scientific control of CTV.

Tuning Synaptic Connections Instead of Weights by Genetic Algorithm in Spiking Policy Network

Learning from interaction is the primary way that biological agents acquire knowledge about their environment and themselves.Modern deep reinforcement learning(DRL)explores a computational approach to learning from interaction and has made significant progress in solving various tasks.However,despite its power,DRL still falls short of biological agents in terms of energy efficiency.Although the underlying mechanisms are not fully understood,we believe that the integration of spiking communication between neurons and biologically-plausible synaptic plasticity plays a prominent role in achieving greater energy efficiency.Following this biological intuition,we optimized a spiking policy network(SPN)using a genetic algorithm as an energy-efficient alternative to DRL.Our SPN mimics the sensorimotor neuron pathway of insects and communicates through event-based spikes.Inspired by biological research showing that the brain forms memories by creating new synaptic connections and rewiring these connections based on new experiences,we tuned the synaptic connections instead of weights in the SPN to solve given tasks.Experimental results on several robotic control tasks demonstrate that our method can achieve the same level of performance as mainstream DRL methods while exhibiting significantly higher energy efficiency.

Analysis of the diversity and function of the alleles of the rice blast resistance genes Piz-t, Pita and Pik in 24 rice cultivars

Understanding the sequence diversity of rice blast resistance genes is important for breeding new resistant rice cultivars against the rice blast fungusMagnaporthe oryzae. In this study, we selected 24 rice cultivars with different genetic back-grounds to study the alelic diversity of rice blast resistance genesPiz-t, Pitaand Pik. For Piz-t, a total of 17 alelic types were found within the 24 cultivars. Blast inoculations showed that most of the mutations can affect the function of the resistance gene. For Pita, except for the difference at the 918th amino acid, a majority of the 21 mutations were detected among the cultivars. Inoculations with blast isolates carryingAvr-Pita revealed that cultivars with mutations in other sites except for the 918th amino acid did not affect the function of thePita gene. ForPik, a total of six alelic types were found within the 24 cultivars, but ifve of them lost the function of the resistance gene. In addition, we found thatPiz-t, Pita and Pik were expressed constitutively in the 24 rice cultivars and the expression level was not related to resistance. Our results have provided the sequence diversity information of the resistance genesPiz-t, Pita and Pik among the popular rice cultivars grown in the northeast region of China. Keywords：resistance gene, avirulence gene, aleles, function, genetic evolution zae（M. oryzae）, is one of the most destructive diseases in rice production worldwide. Over the years, comprehensive studies on rice blast resistance have been conducted （Silue et al. 1992）. The resistance in newly cultivated rice cultivars to M. oryzae can be lost quickly due to the high level of instability in the genome of the fungus （Bonmanet al. 1992）. Previous studies show that cultivars with durable and broad-spectrum resistance againstM. oryzae carry multiple major resistance （R） and minor resistance genes （Liuet al. 2014）. An effective way to control rice blast disease is, therefore, to breed rice cultivars with multiple R and QTL genes. To date, over 83 rice blast R genes have been identiifed, and are distributed on 11 rice chromosomes except Received 22 May, 2015 Accepted 26 October, 2015 WANG Yan, E-mail： 8806wy@163.com; Correspondence LIU Zhi-heng, Tel： ＋86-24-23738857, E-mail： lzhh1954@163.com; ZHENG Wen-jing, Tel： ＋86-24-31021081, E-mail： zwj27@126. com ＊These authors contributed equaly to this study. ？ 2016, CAAS. Al rights reserved. Published by Elsevier Ltd. doi： 10.1016/S2095-3119（15）61207-2 1. Introduction Rice blast disease, caused by the fungusMagnaporthe ory-

Optimized LDPC differential-encoded 16QAM scheme for high-speed transmission systems

The 16-ary quadrature amplitude modulation （16QAM） is a high spectral efficient scheme for high-speed transmission systems. To remove the phase ambiguity in the coherent detection system, differential-encoded 16QAM （DE-16QAM） is usually used, however, it will cause performance degradation about 3 dB as compared to the conventional 16QAM. To overcome the performance loss, a serial concatenated system with outer low density parity check （LDPC） codes and inner DE-16QAM is proposed. At the receiver, joint iterative differential demodulation and decoding （ID） is carried out to approach the maximum likelihood performance. Moreover, a genetic evolution algorithm based on the extrinsic information transfer chart is proposed to optimize the degree distribution of the outer LDPC codes. Both theoretical analyses and simulation results indicate that this algorithm not only compensates the performance loss, but also obtains a significant performance gain, which is up to 1 dB as compared to the conventional non-DE-16QAM.

Expression and contribution of microphthalmia-associated transcription factor to the melanin deposition in Liancheng white ducks

The present study investigates the expression of microphthalmia-associated transcription factor(MITF) and its contribution to the melanin deposition in Liancheng white ducks.Nested PCR was used to clone the MITF gene sequence from the skin tissue of female Liancheng white ducks.Ultraviolet spectrophotometry was used to detect the melanin deposition.MITF mRNA expression and melanin deposition in different tissues and organs were detected and their correlation was analyzed.The MITF gene(GenBank number: MG516570) was 1 323 bp in length,contains a complete CDS region(34-1 323 bp) and codes 429 amino acids with 100% homology to the MITF of Anas platyrhynchos and over 95% homology to those of Gallus gallus and Coturnix japonica.Genetic evolution analysis reveals a close relationship of Liancheng white ducks with A.platyrhynchos,and also to lesser extents with Anser cygnoides,silky fowl and G.gallus,as well as Sus scrofa,Ovis aries and other mammals.Real-time quantitative PCR(qPCR) analysis demonstrated that MITF was expressed in skin,gizzard,liver,kidney and muscle,and of these tissues,its expression was the highest in the skin tissue(skin>gizzard>liver>kidney>muscle).Ultraviolet spectrophotometry showed that melanin deposition was positively correlated with the MITF expression level in these five tissues and organs(P<0.05).Together,these results demonstrated a tissue-specific pattern of MITF expression and a positive correlation between MITF expression and melanin deposition,indicating that MITF expression may contribute to the melanin deposition in Liancheng white ducks.

Genetic variability and evolution of rice stripe virus

Rice stripe virus(RSV) is the type member of the genus Tenuivirus.RSV is known to have four segmented,single-stranded RNA molecules and causes rice stripe disease in the rice fields of China,Japan,and Korea.Based on the complete genomic sequences of the determined 6 RSV isolates(from Yunnan,Jiangsu,Zhejiang,and Liaoning Provinces,China) and 27 other RSV isolates(from Yunnan,Jiangsu,Anhui,Henan,and Shandong Provinces of China,also Japan and Korea) downloaded from GenBank,we provided a genotyping profile of RSV field isolates and described the population structure of RSV.All RSV isolates,except isolate CX,could be divided into two subtypes,one including 6 isolates from Yunnan Province,and the other including 26 isolates from different parts of China,Japan,and Korea,which were referred to as subtype II and subtype I,respectively.The amino acid distances between subtypes range from 0.053 to 0.085.RSV isolates in Yunnan Province were genetically differentiated from other parts of China,Japan,and Korea and showed infrequent gene flow.The RSV populations collected from other parts of China,Japan,and Korea were only composed of subtype I and showed very low genetic diversity.We speculated that isolate CX may be the result of recombination of isolates from two subtypes.Two potential recombination events were detected in RNA4 of isolate CX.

Relatively rapid evolution rates of SARS-CoV-2 spike gene at the primary stage of massive vaccination

A series of stringent non-pharmacological and pharmacological interventions were implemented to contain the pandemic but the pandemic continues.Moreover,vaccination breakthrough infection and reinfection in convalescent coronavirus disease 2019(COVID-19)cases have been reported.Further,severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variants emerged with mutations in spike(S)gene,the target of most current vaccines.Importantly,the mutations exhibit a trend of immune escape from the vaccination.Herein the scientific question that if the vaccination drives genetic or antigenic drifts of SARS-CoV-2 remains elusive.We performed correlation analyses to uncover the impacts of wide vaccination on epidemiological characteristics of COVID-19.In addition,we investigated the evolutionary dynamics and genetic diversity of SARS-CoV-2 under immune pressure by utilizing the Bayesian phylodynamic inferences and the lineage entropy calculation respectively.We found that vaccination coverage was negatively related to the infections,severe cases,and deaths of COVID-19 respectively.With the increasing vaccination coverage,the lineage diversity of SARS-CoV-2 dampened,but the rapid mutation rates of the S gene were identified,and the vaccination could be one of the explanations for driving mutations in S gene.Moreover,new epidemics resurged in several countries with high vaccination coverage,questioning their current pandemic control strategies.Hence,integrated vaccination and non-pharmacological interventions are critical to control the pandemic.Furthermore,novel vaccine preparation should enhance its capabilities to curb both disease severity and infection possibility.

Accelerated Evolution of H7N9 Subtype Influenza Virus under Vaccination Pressure

No avian H7 N9 outbreaks have occurred since the introduction of H7 N9 inactivated vaccine in the fall of 2017.However,H7 N9 is still prevalent in poultry.To surveil the prevalence,genetic characteristics,and antigenic changes of H7 N9,over7000 oropharyngeal and cloaca swab specimens were collected from live poultry markets and farms in 15 provinces of China from 2017 to 2019.A total of 85 influenza virus subtype H7 N9 strains were isolated and 20 representative strains were selected for genetic analysis and antigenicity evaluation.Results indicated the decreased prevalence of low-pathogenic H7 N9 strains while highly-pathogenic H7 N9 strains became dominated since the introduction of vaccine.Phylogenetic analysis showed that strains from 2019 formed an independent small branch and were genetically distant to strains isolated in 2013–2018.Analysis of key amino acid sites showed that the virus strains may adapt to the host environment evolutionally through mutation.Our analysis predicted additional potential glycosylation sites for HA and NA genes in the 2019 strains.Sequence analysis of HA gene in strains isolated from 2018 to 2019 showed that there were an increased nucleotide substitution rate and an increased mutation rate in the first and second nucleotides of coding codons within the open reading frame.The hemagglutination inhibition(HI)assay showed that H7-Re1 and H7-Re2 exhibited a lower HI titer for isolates from 2019,while H7-Re3 and r LN79 showed a high HI titer.The protective effect of the vaccine decreased after15 months of use.Overall,under vaccination pressure,the evolution of influenza virus subtype H7 N9 has accelerated.

Molecular epidemiology of coxsackievirus A16 circulating in children in Beijing, China from 2010 to 2019

Background Coxsackievirus A16(CVA16)is one of the major etiological agents of hand,foot and mouth discase(HFMD).This study aimed to investigate the molecular epidemiology and evolutionary characteristics of CVA16.Methods Throat swabs were collected from children with HFMD and suspected HFMD during 2010-2019.Enteroviruses(EVs)were detected and typed by real-ime reverse transcription-polymerase chain reaction(RT-PCR)and RT-PCR.The genotype,evolutionary rate,the most recent common ancestor,population dynamics and selection pressure of CVA16 were analyzed based on viral protein gene(VPI)by bioinformatics software.Results A total of 4709 throat swabs were screened.EVs were detected in 3180 samples and 814 were CVA16 positive.More than 81%of CVA 16-positive children were under 5 years old.The prevalence of CVA 16 showed obvious periodic fluctuations with a high level during 2010--2012 followed by an apparent decline during 2013--2017.However,the activities of CVA16 increased gradually during 2018-2019.All the Beijing CVA16 strains belonged to sub-genotype BI,and B Ib was the dominant strain.One B Ic strain was detected in Bejing for the first time in 2016.The estimated mean evolutionary rate of VPI gene was 4.49x 103 substitution/site/year.Methionine gradually fixed at site-23 of VP1 since 2012.Two sites were detected under episodic positive selection,one of which(site-223)located in neutralizing linear epitope PEP71.Conclusions The dominant strains of CVA 16 belonged to clade B lb and evolved in a fast evolutionary rate during 2010-2019 in Beiing.To provide more favorable data for HFMD prevention and control,it is necessary to keep attention on molecular epidemiological and evolutionary characteristics of CVA16.

Evidence for the paternal mitochondrial DNA in the crucian carp-like fish lineage with hybrid origin

In terms of taxonomic status,common carp(Cyprinus carpio,Cyprininae)and crucian carp(Carassius auratus,Cyprininae)are different species;however,in this study,a newborn homodiploid crucian carp-like fish(2n=100)(2nNCRC)lineage(F1–F3)was established from the interspecific hybridization of female common carp(2n=100)×male blunt snout bream(Megalobrama amblycephala,Cultrinae,2n=48).The phenotypes and genotypes of 2 n NCRC differed from those of its parents but were closely related to those of the existing diploid crucian carp.We further sequenced the whole mitochondrial(mt)genomes of the 2n NCRC lineage from F1 to F3.The paternal mt DNA fragments were stably embedded in the mt-genomes of F1–F3 generations of 2n NCRC to form chimeric DNA fragments.Along with this chimeric process,numerous base sites of F1–F3 generations of 2 n NCRC underwent mutations.Most of these mutation sites were consistent with the existing diploid crucian carp.Moreover,the mt DNA organization and nucleotide composition of 2n NCRC were more similar to those of the existing diploid crucian carp than those of the parents.The inheritable chimeric DNA fragments and mutant loci in the mt-genomes of different generations of 2nNCRC provided important evidence of the mt DNA change process in the newborn lineage derived from hybridization of different species.Our findings demonstrated for the first time that the paternal mt DNA were transmitted into the mt-genomes of homodiploid lineage,which provided new insights into the existence of paternal mt DNA in the mt DNA inheritance.