Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
As a key component of the plant antioxidant enzymatic system,superoxide dismutase(SOD)can efficiently protect cells from oxidative stress and maintain redox homeostasis.Currently,there are few studies related to SOD g...As a key component of the plant antioxidant enzymatic system,superoxide dismutase(SOD)can efficiently protect cells from oxidative stress and maintain redox homeostasis.Currently,there are few studies related to SOD genes in various taxa of algae,and the specific functions and evolutionary patterns of these family members remain unclear.In this study,comprehensively evolutionary analysis of SOD gene family in the bladed Bangiales was carried out.A total of 9,10,and 12 SOD genes were identified from three species of Pophyra umbilicalis,Pyropia haitanensis,and Pyropia yezoensis,respectively.Based on phylogenetic analysis,SOD gene members within the same subfamily exhibited similar motif patterns as well as conserved domains,which could be attribute to Cu/Zn-SOD and Fe/Mn-SOD.The promoter regions of SOD genes were rich in hormone-responsive,stress-responsive,and growth cis-acting elements,with variations and similarities observed among different species of other red algae and subfamilies.According to subcellular location prediction,it is suggested that Cu/Zn-SOD was predominantly located in chloroplasts,while Fe/Mn-SOD was primarily located in mitochondria.Also,the two subfamilies differed significantly in the two-/three-dimensional protein structures.In terms of gene evolution,the strongest collinearity relationship was shown between Pyropia haitanensis and Pyropia yezoensis,with all the 1꞉1 orthologous gene pair being subjected to a purifying selection(Ka/Ks<1,Ka:non-synonymy rate;Ks:synonymy rate).Moreover,12 SOD genes underwent positive selection during the evolutionary process.Furthermore,gene expression analysis based on transcriptomic data from Pyropia haitanensis showed that the expression patterns of SOD genes varied under different stress conditions.Together,this study revealed the evolutionary pattern of SOD genes in three bladed Bangiales species,which will lay the foundation for subsequent studies on the function of SOD genes.展开更多
The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global disruption.With the rapid accumulation of SARS-...The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global disruption.With the rapid accumulation of SARS-CoV-2 genome sequences,however,thousands of genomic variants of SARSCoV-2 are now publicly available.To improve the tracing of the viral genomes’evolution during the development of the pandemic,we analyzed single nucleotide variants(SNVs)in 121,618 high-quality SARS-CoV-2 genomes.We divided these viral genomes into two major lineages(L and S)based on variants at sites 8782 and 28144,and further divided the L lineage into two major sublineages(L1 and L2)using SNVs at sites 3037,14408,and 23403.Subsequently,we categorized them into 130 sublineages(37 in S,35 in L1,and 58 in L2)based on marker SNVs at 201 additional genomic sites.This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages.We also provide a companion website(www.covid19evolution.net)that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification.Finally,we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2’s evolution.These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2’s genome evolution.展开更多
On December 7,2022,China adjusted public health control measures,there have been widespread of SARS-CoV-2 infections in Chinese mainland.As the number of infected people increased,the mutation probability of SARS-CoV-...On December 7,2022,China adjusted public health control measures,there have been widespread of SARS-CoV-2 infections in Chinese mainland.As the number of infected people increased,the mutation probability of SARS-CoV-2 is also raised.Therefore,it is of great importance to monitor SARS-CoV-2 variants and its mutations in China.In this current study,665 SARS-CoV-2 genomes from China deposited in the public database were used to analyze the proportion of different variants;to determine the composition of variants in China across different provinces;and analyze specific mutation frequency,focusing on 12 immune escape residues.The results showed that no new mutations were generated on the 12 immune escape residues.The evolutionary analysis of the BF.7 variant circulating in China showed that there is an independent evolutionary branch with unique mutation sites,officially named BF.7.14 by PANGO.This variant may have been imported from Russia to Inner Mongolia at the end of September 2022 and continued its spread in China.The evolutionary analysis of BA.5.2 variant shows that the variant is composed of two sub-variants,named BA.5.2.48 and BA.5.2.49 by PANGO,respectively.This variant may have been imported from abroad to Beijing at the beginning of September 2022 and formed two sub-variants after domestic transmission.Finally,this study showed that current epidemic variants in China were already circulating in other countries,and there were no additional mutations on immune escape residues that could pose a threat to other countries.展开更多
Oct4 is one of the key pluripotent factors essential for embryonic stem cells and induced pluripotent stem （iPS） cells. Oct4 belongs to the POU domain family, which contains multiples genes with various important fu...Oct4 is one of the key pluripotent factors essential for embryonic stem cells and induced pluripotent stem （iPS） cells. Oct4 belongs to the POU domain family, which contains multiples genes with various important functions. Although the function of Oct4 has been extensively studied, detailed comparison of Oct4 with other POU family genes and their evolutionary analysis are still lacking. Here, we systematically identified POU family genes from lower to higher animal species. We observed an expansion of POU family genes in vertebrates, with an additional increment in mammalian genomes. We analyzed the phylogenetic relationship, tissue specific expression profiles and regulatory networks of POU family genes of the human genome, and predicted the putative binding microRNAs of human POU family genes. These results provide the first comprehensive evolutionary and comparative analysis of POU family genes, which will help to better understand the relationships among POU family genes and shed light on their future functional studies.展开更多
Objective:To evaluate the evolution of the pathogen Mayaro virus,causing Mayaro fever(a mosquito-borne disease)and to perform selective pressure analysis and homology modelling.Methods:Nine different datasets were bui...Objective:To evaluate the evolution of the pathogen Mayaro virus,causing Mayaro fever(a mosquito-borne disease)and to perform selective pressure analysis and homology modelling.Methods:Nine different datasets were built,one for each protein(from protein C to non-structural protein 4)and the last one for the complete genome.Selective pressure and homology modelling analyses were applied.Results:Two main clades(A and B)were pointed in the maximum likelihood tree.The clade A included five Brazilian sequences sampled from 1955 to 2015.The Brazilian sequence sampled in 2014 significantly clustered with the Haitian sequence sampled in 2015.The clade B included the remaining 27 sequences sampled in the Central and Southern America from 1957 to 2013.Selective pressure analysis revealed several sites under episodic diversifying selection in envelope surface glycoprotein El,non-structural protein 1 and nonstructural protein 3 with a posterior probability P≤0.01.Homology modelling showed different sites modified by selective pressure and some protein-protein interaction sites at high interaction propensity.Conclusion:Maximum likelihood analysis confirmed the Mayaro virus previous circulation in Haiti and the successful spread to the Caribbean and USA.Selective pressure analysis revealed a strong presence of negatively selected sites,suggesting a probable purging of deleterious polymorphisms in functional genes.Homology model showed the position 31,under selective pressure,located in the edge of the ADP-ribose binding site predicting to possess a high potential of protein-protein interaction and suggesting the possible chance for a protective vaccine,thus preventing Mayaro virus urbanization as with Chikungunya virus.展开更多
Heat shock transcription factors(Hsfs)have important roles during plant growth and development and responses to abiotic stresses.The identification and func-tion of Hsf genes have been thoroughly studied in various he...Heat shock transcription factors(Hsfs)have important roles during plant growth and development and responses to abiotic stresses.The identification and func-tion of Hsf genes have been thoroughly studied in various herbaceous plant species,but not woody species,especially Phoebe bournei,an endangered,unique species in China.In this study,17 members of the Hsf gene family were identi-fied from P.bournei using bioinformatic methods.Phyloge-netic analysis indicated that PbHsf genes were grouped into three subfamilies:A,B,and C.Conserved motifs,three-dimensional structure,and physicochemical properties of the PbHsf proteins were also analyzed.The structure of the PbHsf genes varied in the number of exons and introns.Pre-diction of cis-acting elements in the promoter region indi-cated that PbHsf genes are likely involved in responses to plant hormones and stresses.A collinearity analysis dem-onstrated that expansions of the PbHsf gene family mainly take place via segmental duplication.The expression levels of PbHsf genes varied across different plant tissues.On the basis of the expression profiles of five representative PbHsf genes during heat,cold,salt,and drought stress,PbHsf pro-teins seem to have multiple functions depending on the type of abiotic stress.This systematic,genome-wide investigation of PbHsf genes in P.bournei and their expression patterns provides valuable insights and information for further func-tional dissection of Hsf proteins in this endangered,unique species.展开更多
The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental concerns.Increasing the N use efficiency(NUE)of rice varieties is crucial for sustainable agriculture.Here we repo...The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental concerns.Increasing the N use efficiency(NUE)of rice varieties is crucial for sustainable agriculture.Here we report the cloning and characterization of OsNPF3.1,a gene that controls rice NUE.An amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated rice.OsNPF3.1,which is expressed mainly in the aerial parts of rice,also affects rice plant height,heading date,and thousand-grain weight.The OsNPF3.1 protein is located in the plasma membrane.When OsNPF3.1 was subjected to artificial selection,two naturally varying loci were associated with NUE,of which OsNPF3.1Chr6_8741040differed between indica and japonica rice.OsNPF3.1 can be used as a new target gene for breeding rice varieties with high NUE.展开更多
Members of the activity of bc1 complex (ABC1) family are protein kinases that are widely found in prokaryotes and eukaryotes. Previous studies showed that several plant ABC1 genes participated in the abiotic stress re...Members of the activity of bc1 complex (ABC1) family are protein kinases that are widely found in prokaryotes and eukaryotes. Previous studies showed that several plant ABC1 genes participated in the abiotic stress response. Here, we present the systematic identification of rice and Arabidopsis ABC1 genes and the expression analysis of rice ABC1 genes. A total of 15 and 17 ABC1 genes from the rice and Arabidopsis genomes, respectively, were identified using a bioinformatics approach. Phylogenetic analyses of these proteins suggested that the divergence of this family had occurred and their main characteristics were established before the monocot-dicot split. Indeed, species-specific expansion contributed to the evolution of this family in rice and Arabidopsis after the monocot-dicot split. Intron/exon structure analysis indicated that most of the orthologous genes had similar exon sizes, but diverse intron sizes, and the rice genes contained larger introns, moreover, intron gain was an important event accompanying the recent evolution of the rice ABC1 family. Multiple sequence alignment revealed one conserved amino acid segment and four conserved amino acids in the ABC1 domain. Online subcellular localization predicted that nine rice ABC1 proteins were localized in chloroplasts. Real-time RT-PCR established that the rice ABC1 genes were primarily expressed in leaves and the expression could be modulated by a broad range of abiotic factors such as H2O2, abscisic acid, low temperature, drought, darkness and high salinity. These results reveal that the rice ABC1 gene family plays roles in the environmental stress response and specific biological processes of rice.展开更多
The continuum structural-acoustic topology optimization with external loading is investigated herein. Finite element method （FEM） is used to obtain the structural frequency response and boundary element method （BEM...The continuum structural-acoustic topology optimization with external loading is investigated herein. Finite element method （FEM） is used to obtain the structural frequency response and boundary element method （BEM） is adopted to perform exterior acoustic radiation analysis. The evolutionary structural optimization （ESO） is served as an optimization method in structural-acoustic radiation topology analysis. The acoustic radiation optimization of a plate under harmonic excitation is given for example. The numerical results show that using ESO solution to analyze structural-acoustic topology optimization is feasible and effective.展开更多
Hepatitis B virus(HBV)is categorized into ten distinct genotypes(A-J),with over 4O subgenotypes identified to date.HBV genotype I(HBV-I),an inter-genotypic recombinant,has emerged during the evolution history of HBV.I...Hepatitis B virus(HBV)is categorized into ten distinct genotypes(A-J),with over 4O subgenotypes identified to date.HBV genotype I(HBV-I),an inter-genotypic recombinant,has emerged during the evolution history of HBV.In this study,we conducted a comprehensive analysis of the genomic characteristics of HBV-I in China,employing a range of methodologies including phylogenetic analysis,nucleotide homology assessment,examination of amino acid substitutions within the PreS/S region,recombination detection,and evolutionary analysis.The 12 HBV-I strains,classified into subgenotype I1 and predominantly serotype adw2(with one exception being ayw1)were preliminarily divided into two clusters based on homology analysis.A higher substitution rate was observed in the antigenic loop of the hepatitis B surface antigen(HBsAg),and the potential immune-escape mutations were found.Molecular clock analysis estimated an average evolutionary rate for HBV-I between 1.17 exp(-4)and 1.61 exp(-4)substitutions/site/year,with the most recent common ancestor traced back to between year 1740 and 1774.The epidemiological surveillance and genomic characterization of HBV genotype I are significant for informing future strategies in the prevention and control of hepatitis B.展开更多
Previously we isolated three Fusarium strains(a F.sacchari strain namely GXUF-1,and another two F.commune strains namely GXUF-2 and GXUF-3),and we verified that GXUF-3 was able to cause sugarcane root rot to the chewi...Previously we isolated three Fusarium strains(a F.sacchari strain namely GXUF-1,and another two F.commune strains namely GXUF-2 and GXUF-3),and we verified that GXUF-3 was able to cause sugarcane root rot to the chewing cane cultivar Badila.Considering that Fusarium spp.are a group of widely distributed fungal pathogens,we tested whether these three Fusarium isolates were able to cause root rot to Badila as well as sugar-making cane cultivar(Guitang42),using a suitable inoculation method established based on infection assays using Badila.We found that the three Fusarium strains were able to cause root rot symptoms to both Badila and Guitang42,to different extents.To better investigate the potential pathogenicity mechanisms,we performed Illumina high-throughput sequencing and analyzed the whole genomic sequence data of these three Fusarium strains.The results reveal that the assembly sizes of the three Fusarium strains were in a range of 44.7-48.2 Mb,with G+C contents of 48.0-48.5%,and 14,154-15,175 coding genes.The coding genes were annotated by multiple public databases,and potential pathogenic genes were predicted using proprietary databases(such as PHI,DFVF,CAZy,etc.).Furthermore,based on evolutionary analysis of the coding sequence,we found that contraction and expansion of gene families occurred in the three Fusarium strains.Overall,our results suggest a potential risk that the root rot disease may occur to the sugar-making canes although it was initially spotted from fruit cane,and provide clues to understand the pathogenic mechanisms of Fusarium spp.causing sugarcane root rot.展开更多
Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging.In this study,we developed a sequence-based functional metagenomics procedure for mining the d...Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging.In this study,we developed a sequence-based functional metagenomics procedure for mining the diversity of copper(Cu)resistance gene copA in global microbiomes,by combining the metagenomic assembly technology,local BLAST,evolutionary trace analysis(ETA),chemical synthesis,and conventional functional genomics.In total,87 metagenomes were collected from a public database and subjected to copA detection,resulting in 93,899 hits.Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates,which were further subjected to ETA.Eventually,175 novel copA sequences of high quality were discovered.Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins,with 55 sequences from totally unknown species.Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli(DcopA).The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake.One recombinant harboring copA-like 15(copAL15)successfully restored Cu resistance of the host with a substantially enhanced Cu uptake.Two novel copA genes were fused with the gfp gene and expressed in E.coli for microscopic observation.Imaging results showed that they were successfully expressed and their proteins were localized to the membrane.The results here greatly expand the diversity of known CopA proteins,and the sequence-based procedure developed overcomes biases in length,screening methods,and abundance of conventional functional metagenomics.展开更多
文摘Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
基金Supported by the National Key R&D Program of China(No.2023 YFD 2400102)the Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation,Beibu Gulf University(No.2024 KA 04)。
文摘As a key component of the plant antioxidant enzymatic system,superoxide dismutase(SOD)can efficiently protect cells from oxidative stress and maintain redox homeostasis.Currently,there are few studies related to SOD genes in various taxa of algae,and the specific functions and evolutionary patterns of these family members remain unclear.In this study,comprehensively evolutionary analysis of SOD gene family in the bladed Bangiales was carried out.A total of 9,10,and 12 SOD genes were identified from three species of Pophyra umbilicalis,Pyropia haitanensis,and Pyropia yezoensis,respectively.Based on phylogenetic analysis,SOD gene members within the same subfamily exhibited similar motif patterns as well as conserved domains,which could be attribute to Cu/Zn-SOD and Fe/Mn-SOD.The promoter regions of SOD genes were rich in hormone-responsive,stress-responsive,and growth cis-acting elements,with variations and similarities observed among different species of other red algae and subfamilies.According to subcellular location prediction,it is suggested that Cu/Zn-SOD was predominantly located in chloroplasts,while Fe/Mn-SOD was primarily located in mitochondria.Also,the two subfamilies differed significantly in the two-/three-dimensional protein structures.In terms of gene evolution,the strongest collinearity relationship was shown between Pyropia haitanensis and Pyropia yezoensis,with all the 1꞉1 orthologous gene pair being subjected to a purifying selection(Ka/Ks<1,Ka:non-synonymy rate;Ks:synonymy rate).Moreover,12 SOD genes underwent positive selection during the evolutionary process.Furthermore,gene expression analysis based on transcriptomic data from Pyropia haitanensis showed that the expression patterns of SOD genes varied under different stress conditions.Together,this study revealed the evolutionary pattern of SOD genes in three bladed Bangiales species,which will lay the foundation for subsequent studies on the function of SOD genes.
基金supported by the National Natural Science Foundation of China(91731301 and U1902201)the Ministry of Science and Technology of the People’s Republic of China(2020YFC0847000)the Light of West China Program of the Chinese Academy of Sciences.
文摘The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global disruption.With the rapid accumulation of SARS-CoV-2 genome sequences,however,thousands of genomic variants of SARSCoV-2 are now publicly available.To improve the tracing of the viral genomes’evolution during the development of the pandemic,we analyzed single nucleotide variants(SNVs)in 121,618 high-quality SARS-CoV-2 genomes.We divided these viral genomes into two major lineages(L and S)based on variants at sites 8782 and 28144,and further divided the L lineage into two major sublineages(L1 and L2)using SNVs at sites 3037,14408,and 23403.Subsequently,we categorized them into 130 sublineages(37 in S,35 in L1,and 58 in L2)based on marker SNVs at 201 additional genomic sites.This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages.We also provide a companion website(www.covid19evolution.net)that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification.Finally,we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2’s evolution.These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2’s genome evolution.
基金This work was supported by grants from consultancy project(2022-JB-06)by the Chinese Academy of Engineering(CAE).
文摘On December 7,2022,China adjusted public health control measures,there have been widespread of SARS-CoV-2 infections in Chinese mainland.As the number of infected people increased,the mutation probability of SARS-CoV-2 is also raised.Therefore,it is of great importance to monitor SARS-CoV-2 variants and its mutations in China.In this current study,665 SARS-CoV-2 genomes from China deposited in the public database were used to analyze the proportion of different variants;to determine the composition of variants in China across different provinces;and analyze specific mutation frequency,focusing on 12 immune escape residues.The results showed that no new mutations were generated on the 12 immune escape residues.The evolutionary analysis of the BF.7 variant circulating in China showed that there is an independent evolutionary branch with unique mutation sites,officially named BF.7.14 by PANGO.This variant may have been imported from Russia to Inner Mongolia at the end of September 2022 and continued its spread in China.The evolutionary analysis of BA.5.2 variant shows that the variant is composed of two sub-variants,named BA.5.2.48 and BA.5.2.49 by PANGO,respectively.This variant may have been imported from abroad to Beijing at the beginning of September 2022 and formed two sub-variants after domestic transmission.Finally,this study showed that current epidemic variants in China were already circulating in other countries,and there were no additional mutations on immune escape residues that could pose a threat to other countries.
基金supported by the grants from the Ministry of Science and Technology of China(No.2011CBA01101 to X.-J.W.)the Chinese Academy of Sciences(Nos. XDA01020105,KSCX2-EW-R-01-03 and 2010-Biols-CAS- 0303 to X.-J.W.)
文摘Oct4 is one of the key pluripotent factors essential for embryonic stem cells and induced pluripotent stem （iPS） cells. Oct4 belongs to the POU domain family, which contains multiples genes with various important functions. Although the function of Oct4 has been extensively studied, detailed comparison of Oct4 with other POU family genes and their evolutionary analysis are still lacking. Here, we systematically identified POU family genes from lower to higher animal species. We observed an expansion of POU family genes in vertebrates, with an additional increment in mammalian genomes. We analyzed the phylogenetic relationship, tissue specific expression profiles and regulatory networks of POU family genes of the human genome, and predicted the putative binding microRNAs of human POU family genes. These results provide the first comprehensive evolutionary and comparative analysis of POU family genes, which will help to better understand the relationships among POU family genes and shed light on their future functional studies.
文摘Objective:To evaluate the evolution of the pathogen Mayaro virus,causing Mayaro fever(a mosquito-borne disease)and to perform selective pressure analysis and homology modelling.Methods:Nine different datasets were built,one for each protein(from protein C to non-structural protein 4)and the last one for the complete genome.Selective pressure and homology modelling analyses were applied.Results:Two main clades(A and B)were pointed in the maximum likelihood tree.The clade A included five Brazilian sequences sampled from 1955 to 2015.The Brazilian sequence sampled in 2014 significantly clustered with the Haitian sequence sampled in 2015.The clade B included the remaining 27 sequences sampled in the Central and Southern America from 1957 to 2013.Selective pressure analysis revealed several sites under episodic diversifying selection in envelope surface glycoprotein El,non-structural protein 1 and nonstructural protein 3 with a posterior probability P≤0.01.Homology modelling showed different sites modified by selective pressure and some protein-protein interaction sites at high interaction propensity.Conclusion:Maximum likelihood analysis confirmed the Mayaro virus previous circulation in Haiti and the successful spread to the Caribbean and USA.Selective pressure analysis revealed a strong presence of negatively selected sites,suggesting a probable purging of deleterious polymorphisms in functional genes.Homology model showed the position 31,under selective pressure,located in the edge of the ADP-ribose binding site predicting to possess a high potential of protein-protein interaction and suggesting the possible chance for a protective vaccine,thus preventing Mayaro virus urbanization as with Chikungunya virus.
基金supported by the Fujian Province Seed Industry Innovation and Industrialization Project“Innovation and Industrialization Development of Precious Tree Seed Industries(Phoebe bornei)”(ZYCX-LY-202102)the Sub-project of National Key R&D Program“Phoebe bornei Efficient Cultivation Technology”(2016YFD0600603-2).
文摘Heat shock transcription factors(Hsfs)have important roles during plant growth and development and responses to abiotic stresses.The identification and func-tion of Hsf genes have been thoroughly studied in various herbaceous plant species,but not woody species,especially Phoebe bournei,an endangered,unique species in China.In this study,17 members of the Hsf gene family were identi-fied from P.bournei using bioinformatic methods.Phyloge-netic analysis indicated that PbHsf genes were grouped into three subfamilies:A,B,and C.Conserved motifs,three-dimensional structure,and physicochemical properties of the PbHsf proteins were also analyzed.The structure of the PbHsf genes varied in the number of exons and introns.Pre-diction of cis-acting elements in the promoter region indi-cated that PbHsf genes are likely involved in responses to plant hormones and stresses.A collinearity analysis dem-onstrated that expansions of the PbHsf gene family mainly take place via segmental duplication.The expression levels of PbHsf genes varied across different plant tissues.On the basis of the expression profiles of five representative PbHsf genes during heat,cold,salt,and drought stress,PbHsf pro-teins seem to have multiple functions depending on the type of abiotic stress.This systematic,genome-wide investigation of PbHsf genes in P.bournei and their expression patterns provides valuable insights and information for further func-tional dissection of Hsf proteins in this endangered,unique species.
基金supported by the National Natural Science Foundation of China(32060476 and 31860371)Guangxi Department of Science and Technology(AA22068087-4)+3 种基金Guangxi Natural Science Foundation of China(2015GXNSFAA139054,2018GXNSFAA138124,and 2020GXNSFAA259041)Guangxi Ministry of Science and Technology(AB21238009)Special Fund of Local Science and Technology Development for the Central Guidance(ZY21195034)Guangxi Academy of Agricultural Sciences(2021JM04,2021JM49,2021YT030,QN-25,and QN-35)。
文摘The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental concerns.Increasing the N use efficiency(NUE)of rice varieties is crucial for sustainable agriculture.Here we report the cloning and characterization of OsNPF3.1,a gene that controls rice NUE.An amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated rice.OsNPF3.1,which is expressed mainly in the aerial parts of rice,also affects rice plant height,heading date,and thousand-grain weight.The OsNPF3.1 protein is located in the plasma membrane.When OsNPF3.1 was subjected to artificial selection,two naturally varying loci were associated with NUE,of which OsNPF3.1Chr6_8741040differed between indica and japonica rice.OsNPF3.1 can be used as a new target gene for breeding rice varieties with high NUE.
基金supported by grants from the National Program on the Development of Basic Research of China (Grant No. 2006CB101700)the National Natural Science Foundation of China (Grant No. 30971846)the Vital Project of Natural Science in Universities of Jiangsu Province, China (Grant No. 09KJA210002)
文摘Members of the activity of bc1 complex (ABC1) family are protein kinases that are widely found in prokaryotes and eukaryotes. Previous studies showed that several plant ABC1 genes participated in the abiotic stress response. Here, we present the systematic identification of rice and Arabidopsis ABC1 genes and the expression analysis of rice ABC1 genes. A total of 15 and 17 ABC1 genes from the rice and Arabidopsis genomes, respectively, were identified using a bioinformatics approach. Phylogenetic analyses of these proteins suggested that the divergence of this family had occurred and their main characteristics were established before the monocot-dicot split. Indeed, species-specific expansion contributed to the evolution of this family in rice and Arabidopsis after the monocot-dicot split. Intron/exon structure analysis indicated that most of the orthologous genes had similar exon sizes, but diverse intron sizes, and the rice genes contained larger introns, moreover, intron gain was an important event accompanying the recent evolution of the rice ABC1 family. Multiple sequence alignment revealed one conserved amino acid segment and four conserved amino acids in the ABC1 domain. Online subcellular localization predicted that nine rice ABC1 proteins were localized in chloroplasts. Real-time RT-PCR established that the rice ABC1 genes were primarily expressed in leaves and the expression could be modulated by a broad range of abiotic factors such as H2O2, abscisic acid, low temperature, drought, darkness and high salinity. These results reveal that the rice ABC1 gene family plays roles in the environmental stress response and specific biological processes of rice.
文摘The continuum structural-acoustic topology optimization with external loading is investigated herein. Finite element method （FEM） is used to obtain the structural frequency response and boundary element method （BEM） is adopted to perform exterior acoustic radiation analysis. The evolutionary structural optimization （ESO） is served as an optimization method in structural-acoustic radiation topology analysis. The acoustic radiation optimization of a plate under harmonic excitation is given for example. The numerical results show that using ESO solution to analyze structural-acoustic topology optimization is feasible and effective.
基金supported by the National Key Research and Development Program of China(Grant No.2023YFC2306900).
文摘Hepatitis B virus(HBV)is categorized into ten distinct genotypes(A-J),with over 4O subgenotypes identified to date.HBV genotype I(HBV-I),an inter-genotypic recombinant,has emerged during the evolution history of HBV.In this study,we conducted a comprehensive analysis of the genomic characteristics of HBV-I in China,employing a range of methodologies including phylogenetic analysis,nucleotide homology assessment,examination of amino acid substitutions within the PreS/S region,recombination detection,and evolutionary analysis.The 12 HBV-I strains,classified into subgenotype I1 and predominantly serotype adw2(with one exception being ayw1)were preliminarily divided into two clusters based on homology analysis.A higher substitution rate was observed in the antigenic loop of the hepatitis B surface antigen(HBsAg),and the potential immune-escape mutations were found.Molecular clock analysis estimated an average evolutionary rate for HBV-I between 1.17 exp(-4)and 1.61 exp(-4)substitutions/site/year,with the most recent common ancestor traced back to between year 1740 and 1774.The epidemiological surveillance and genomic characterization of HBV genotype I are significant for informing future strategies in the prevention and control of hepatitis B.
基金supported by National Natural Science Foundation of China(U23A20148)Key Projects of Guangzhou Science and Technology Plan(201904020010)。
文摘Previously we isolated three Fusarium strains(a F.sacchari strain namely GXUF-1,and another two F.commune strains namely GXUF-2 and GXUF-3),and we verified that GXUF-3 was able to cause sugarcane root rot to the chewing cane cultivar Badila.Considering that Fusarium spp.are a group of widely distributed fungal pathogens,we tested whether these three Fusarium isolates were able to cause root rot to Badila as well as sugar-making cane cultivar(Guitang42),using a suitable inoculation method established based on infection assays using Badila.We found that the three Fusarium strains were able to cause root rot symptoms to both Badila and Guitang42,to different extents.To better investigate the potential pathogenicity mechanisms,we performed Illumina high-throughput sequencing and analyzed the whole genomic sequence data of these three Fusarium strains.The results reveal that the assembly sizes of the three Fusarium strains were in a range of 44.7-48.2 Mb,with G+C contents of 48.0-48.5%,and 14,154-15,175 coding genes.The coding genes were annotated by multiple public databases,and potential pathogenic genes were predicted using proprietary databases(such as PHI,DFVF,CAZy,etc.).Furthermore,based on evolutionary analysis of the coding sequence,we found that contraction and expansion of gene families occurred in the three Fusarium strains.Overall,our results suggest a potential risk that the root rot disease may occur to the sugar-making canes although it was initially spotted from fruit cane,and provide clues to understand the pathogenic mechanisms of Fusarium spp.causing sugarcane root rot.
基金supported by the National Natural Science Foundation of China(Grant No.41877414)the National Key R&D Program of China(Grant No.2018YFD0800306)+3 种基金the Hebei Provincial Science Fund for Distinguished Young Scholars(Grant No.D2018503005)supported by the National Natural Science Foundation of China(Grant No.31700228)supported by the National Natural Science Foundation of China(Grant No.U21A20182)the Youth Innovation Promotion Association,Chinese Academy of Sciences(Grant No.2021092).
文摘Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging.In this study,we developed a sequence-based functional metagenomics procedure for mining the diversity of copper(Cu)resistance gene copA in global microbiomes,by combining the metagenomic assembly technology,local BLAST,evolutionary trace analysis(ETA),chemical synthesis,and conventional functional genomics.In total,87 metagenomes were collected from a public database and subjected to copA detection,resulting in 93,899 hits.Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates,which were further subjected to ETA.Eventually,175 novel copA sequences of high quality were discovered.Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins,with 55 sequences from totally unknown species.Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli(DcopA).The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake.One recombinant harboring copA-like 15(copAL15)successfully restored Cu resistance of the host with a substantially enhanced Cu uptake.Two novel copA genes were fused with the gfp gene and expressed in E.coli for microscopic observation.Imaging results showed that they were successfully expressed and their proteins were localized to the membrane.The results here greatly expand the diversity of known CopA proteins,and the sequence-based procedure developed overcomes biases in length,screening methods,and abundance of conventional functional metagenomics.
