Porcine reproductive and respiratory syndrome(PRRS)is a problem that has significant economic impact on the global pig industry.In recent years,there has been an increased importation of pork into China,contributing t...Porcine reproductive and respiratory syndrome(PRRS)is a problem that has significant economic impact on the global pig industry.In recent years,there has been an increased importation of pork into China,contributing to the emergence of novely imported porcine reproductive and respiratory syndrome virus(PRRSV)sub-types.Nevertheless,codon usage patterns and their effects on the evolution and adaptation of these new input PRRSV sub-types in hosts remain elusive.To investigate this,we employed a Bayesian approach to analyze two novel imported PRRSV sub-types,namely,NADC30-like and NADC34-like viruses.These sub-types have different codon preferences.Besides,the Effective Number of Codon(ENC)analysis revealed that both NADC30-like and NADC34-like fall within the expected curve distribution,describing a balanced codon usage for both NADC30-like and NADC34-like virus.Based on the Codon Adaptation Index(CAI),NADC30-like showed the highest similarity to the host,aligning with the main prevalence trend of the host.In contrast,NADC34-like exhibited the highest frequency of optimal codon usage;this analysis is based on Frequency of Optimal Codons(FOP).Moreover,the Relative Codon Deoptimization Index(RCDI)indicates that NADC30-like sub-types have a greater degree of inverse optimization sub-type.These findings suggest that mutational pressure affects codon usage preferences of genes in newly imported PRRSV,and that natural selection plays a vital role in determining PRRSV gene codon preferences.Our study provides new insights into the disease,origin,evolutionary patterns,and host adaptation of these newly imported PRRSV sub-types in China.It also contributes to the development of theoretical frameworks for studying genetics and the evolution of PRRSV.展开更多
Tremella fuciformis,one of the most approved mushrooms worldwide,possesses both edible and medicinal value.However,low transformation efficiency and high false positive rate,long verification period,and low expression...Tremella fuciformis,one of the most approved mushrooms worldwide,possesses both edible and medicinal value.However,low transformation efficiency and high false positive rate,long verification period,and low expression of heterologous proteins hinder further genetic research.In this study,a polyethylene glycol-mediated genetic transformation system was established by using the homologous resistance marker carboxin in T.fuciformis.By optimizing the protoplast quality and transformation conditions,the transformation efficiency reached 8.23 CFU/μg,and the positive rate reached 64.95%.Moreover,Driselase-Heating-Freezing screening system was developed for rapid transformants verification,which took only 35-45 min and made the colony PCR 100%accurate.Considering the rationality of tRNA use frequency in heterologous genes,the coordinated relative synonymous codon usage(RSCU)strategy was adopted to recode the heterologous gene sequence,which ensured the protein expression level.This study comprehensively enhances molecular biology tools in T.fuciformis,and lays a foundation for further development.展开更多
基金supported by the Postdoctoral Science Foundation 72nd Grant of China(2022M723906)Projects of Jilin Province Science and Technology Development Plan(20220508051RC).
文摘Porcine reproductive and respiratory syndrome(PRRS)is a problem that has significant economic impact on the global pig industry.In recent years,there has been an increased importation of pork into China,contributing to the emergence of novely imported porcine reproductive and respiratory syndrome virus(PRRSV)sub-types.Nevertheless,codon usage patterns and their effects on the evolution and adaptation of these new input PRRSV sub-types in hosts remain elusive.To investigate this,we employed a Bayesian approach to analyze two novel imported PRRSV sub-types,namely,NADC30-like and NADC34-like viruses.These sub-types have different codon preferences.Besides,the Effective Number of Codon(ENC)analysis revealed that both NADC30-like and NADC34-like fall within the expected curve distribution,describing a balanced codon usage for both NADC30-like and NADC34-like virus.Based on the Codon Adaptation Index(CAI),NADC30-like showed the highest similarity to the host,aligning with the main prevalence trend of the host.In contrast,NADC34-like exhibited the highest frequency of optimal codon usage;this analysis is based on Frequency of Optimal Codons(FOP).Moreover,the Relative Codon Deoptimization Index(RCDI)indicates that NADC30-like sub-types have a greater degree of inverse optimization sub-type.These findings suggest that mutational pressure affects codon usage preferences of genes in newly imported PRRSV,and that natural selection plays a vital role in determining PRRSV gene codon preferences.Our study provides new insights into the disease,origin,evolutionary patterns,and host adaptation of these newly imported PRRSV sub-types in China.It also contributes to the development of theoretical frameworks for studying genetics and the evolution of PRRSV.
基金supported by the National Key Research and Development Program of China(No.2019YFA0905200)the National Natural Science Foundation of China(No.22178177)+1 种基金the Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture(No.XTD2201)the Jiangsu Funding Program for Excellent Postdoctoral Talent(2023ZB445).
文摘Tremella fuciformis,one of the most approved mushrooms worldwide,possesses both edible and medicinal value.However,low transformation efficiency and high false positive rate,long verification period,and low expression of heterologous proteins hinder further genetic research.In this study,a polyethylene glycol-mediated genetic transformation system was established by using the homologous resistance marker carboxin in T.fuciformis.By optimizing the protoplast quality and transformation conditions,the transformation efficiency reached 8.23 CFU/μg,and the positive rate reached 64.95%.Moreover,Driselase-Heating-Freezing screening system was developed for rapid transformants verification,which took only 35-45 min and made the colony PCR 100%accurate.Considering the rationality of tRNA use frequency in heterologous genes,the coordinated relative synonymous codon usage(RSCU)strategy was adopted to recode the heterologous gene sequence,which ensured the protein expression level.This study comprehensively enhances molecular biology tools in T.fuciformis,and lays a foundation for further development.
