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
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...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.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
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(NSFC):(Grant No.32002268)the China Postdoctoral Science Foundation(Grant No.2019M662677)the Wuhan 3551 Optics Valley Talent Program and the Wuhan Talent Program.
文摘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.
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.
