基因氨基酸编码区的核苷酸具有不同替代速率.同义替代不引起氨基酸改变,它们基本是中性替代速率;非同义替代引起氨基酸变化,替代速率常常比同义替代速率低.非同义(或同义)替代速率定义为单位时间(如1年)内或者一个世代内1个非同义(或同...基因氨基酸编码区的核苷酸具有不同替代速率.同义替代不引起氨基酸改变,它们基本是中性替代速率;非同义替代引起氨基酸变化,替代速率常常比同义替代速率低.非同义(或同义)替代速率定义为单位时间(如1年)内或者一个世代内1个非同义(或同义)位点上发生替代的数目,用符号dN(或dS)来表示.生物体内发生的非同义突变大多数属于有害突变,只有少数是中性突变或有利突变.对有害的非同义突变来说,dN-dS<1;而对于有利的非同义突变来说,dN-dS>1.仅仅通过比较dN和dS还不能确定是否就一定受到选择作用,还必须用统计学的方法来检验它们的真实性和可靠性.计算dN和dS的方法有多种,常见的是4种:N-G模型、改进的N-G模型、Li-Wu-Luo模型和P-B-Li模型.4种方法从不同的角度计算编码区核苷酸的dN,dS值,它们各有特点,适合不同基因的计算.对dN,dS值进行统计检验的方法也有多种,常见的方法有5种:Z检验、Tajima’s D检验F、u and Li检验、HKA检验和MK检验.这5种检验方法也各有特点,适合不同基因dN,dS值的检验.展开更多
核苷酸替代和indels(插入、缺失统称)发生是进化的重要动力。以茄科植物为研究对象,探讨茄属中番茄和马铃薯、烟草属中绒毛状烟草和普通烟草分化时叶绿体基因组indels和核苷酸替代的发生方式,以及这两种突变对基因组造成的影响。结果显...核苷酸替代和indels(插入、缺失统称)发生是进化的重要动力。以茄科植物为研究对象,探讨茄属中番茄和马铃薯、烟草属中绒毛状烟草和普通烟草分化时叶绿体基因组indels和核苷酸替代的发生方式,以及这两种突变对基因组造成的影响。结果显示:indels和核苷酸替代的发生都不是随意的。indels发生在A+T丰富的区域,1 bp indels占据总数的30%以上,大部分indels都为低于10bp的较短片段。核苷酸替代表现出Ts(转换)/Tv(颠换)偏差,但T→G,A→C颠换频率却明显增加。Ts/Tv比值出现种属特异性,番茄和马铃薯比较时替代的Ts/Tv比值低于绒毛状烟草和普通烟草比较时Ts/Tv比值。不同物种替代的(A+T)/(G+C)比值有一定差异,从而影响基因组的(G+C)%,此比值的差异与形成物种的生长习性有一定的关系。展开更多
Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular...Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.展开更多
[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 ...[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.展开更多
The study of nucleotide substitution is very important both to our understanding of gene evolution and to reliable estimation of phylogenetic relationships. In this paper nucleotide substitution is assumed to be ran...The study of nucleotide substitution is very important both to our understanding of gene evolution and to reliable estimation of phylogenetic relationships. In this paper nucleotide substitution is assumed to be random and the Markov model is applied to the study of the evolution of genes. Then a non linear optimization approach is proposed for estimating substitution in real sequences. This substitution is called the 'Nucleotide State Transfer Matrix'. One of the most important conclusions from this work is that gene sequence evolution conforms to the Markov process. Also, some theoretical evidences for random evolution are given from energy analysis of DNA replication.展开更多
Rice grain size is an important trait that affects rice yield and quality, and thus the identification of genes related to grain size is of great significance for improving rice yield and quality. Many genes related t...Rice grain size is an important trait that affects rice yield and quality, and thus the identification of genes related to grain size is of great significance for improving rice yield and quality. Many genes related to grain size, such as DEP1(Huang et al., 2009),GW5(Liu et al., 2017).展开更多
文摘基因氨基酸编码区的核苷酸具有不同替代速率.同义替代不引起氨基酸改变,它们基本是中性替代速率;非同义替代引起氨基酸变化,替代速率常常比同义替代速率低.非同义(或同义)替代速率定义为单位时间(如1年)内或者一个世代内1个非同义(或同义)位点上发生替代的数目,用符号dN(或dS)来表示.生物体内发生的非同义突变大多数属于有害突变,只有少数是中性突变或有利突变.对有害的非同义突变来说,dN-dS<1;而对于有利的非同义突变来说,dN-dS>1.仅仅通过比较dN和dS还不能确定是否就一定受到选择作用,还必须用统计学的方法来检验它们的真实性和可靠性.计算dN和dS的方法有多种,常见的是4种:N-G模型、改进的N-G模型、Li-Wu-Luo模型和P-B-Li模型.4种方法从不同的角度计算编码区核苷酸的dN,dS值,它们各有特点,适合不同基因的计算.对dN,dS值进行统计检验的方法也有多种,常见的方法有5种:Z检验、Tajima’s D检验F、u and Li检验、HKA检验和MK检验.这5种检验方法也各有特点,适合不同基因dN,dS值的检验.
文摘核苷酸替代和indels(插入、缺失统称)发生是进化的重要动力。以茄科植物为研究对象,探讨茄属中番茄和马铃薯、烟草属中绒毛状烟草和普通烟草分化时叶绿体基因组indels和核苷酸替代的发生方式,以及这两种突变对基因组造成的影响。结果显示:indels和核苷酸替代的发生都不是随意的。indels发生在A+T丰富的区域,1 bp indels占据总数的30%以上,大部分indels都为低于10bp的较短片段。核苷酸替代表现出Ts(转换)/Tv(颠换)偏差,但T→G,A→C颠换频率却明显增加。Ts/Tv比值出现种属特异性,番茄和马铃薯比较时替代的Ts/Tv比值低于绒毛状烟草和普通烟草比较时Ts/Tv比值。不同物种替代的(A+T)/(G+C)比值有一定差异,从而影响基因组的(G+C)%,此比值的差异与形成物种的生长习性有一定的关系。
基金supported by the National Natural Science Foundation of China (Grant Nos. 30570008 and 30770012) the Chinese Academy of Sciences (Grant No. KSCX2-YW-Z-041)
文摘Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.
基金Supported by Natural Science Foundation of Jiangsu Province(BK2009235)~~
文摘[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.
文摘The study of nucleotide substitution is very important both to our understanding of gene evolution and to reliable estimation of phylogenetic relationships. In this paper nucleotide substitution is assumed to be random and the Markov model is applied to the study of the evolution of genes. Then a non linear optimization approach is proposed for estimating substitution in real sequences. This substitution is called the 'Nucleotide State Transfer Matrix'. One of the most important conclusions from this work is that gene sequence evolution conforms to the Markov process. Also, some theoretical evidences for random evolution are given from energy analysis of DNA replication.
基金supported by the grants from the National Key Research and Development Program of China (2016YFD0100406)the Rice Molecular Design Breeding (2016YFD0101801)+1 种基金the National Natural Science Foundation of China (91535102 and 31771760)the Open Research Fund of State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center) (2016KF09)
文摘Rice grain size is an important trait that affects rice yield and quality, and thus the identification of genes related to grain size is of great significance for improving rice yield and quality. Many genes related to grain size, such as DEP1(Huang et al., 2009),GW5(Liu et al., 2017).
