Since late 2011,outbreaks of pseudorabies virus(PRV)have occurred in southern China causing major economic losses to the pig industry.We previously reported that variant PRV forms and recombination in China could be t...Since late 2011,outbreaks of pseudorabies virus(PRV)have occurred in southern China causing major economic losses to the pig industry.We previously reported that variant PRV forms and recombination in China could be the source of continued epidemics.Here,we analyzed samples from intensive pig farms in eastern China between 2017 and 2019,and sequenced the main glycoproteins(gB,gC,gD,and gE)to study the evolution characteristics of PRV.Based on the gC gene,we found that PRV variants belong to clade 2 and detected a founder effect during by the PRV epidemic.In addition,we detected inter-and intra-clade recombination;in particular,inter-clade recombination in the gB genes of strains FJ-ZXF and FJ-W2,which were recombinant with clade 1 strains.We also found specific amino-acid changes and positively selected sites,possibly associated with functional changes.This analysis of the emergence of PRV in China illustrates the need for continuous monitoring and the development of vaccines against specific variants of PRV.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
On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps u...On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps under a climate with freezing winter cold. These findings lead us to-examine the past ideas about domestication and differentiation of rice. Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Soon after that, the two types were classified by the associations of a number of genetically independent traits. The characteristic associations of traits have been explained by the hybrid sterility or reproductive barriers which were assumed to comprise a set of duplicate recessive lethal genes and to be an inner genetic mechanism to lead to the varietal differentiations In 1980s, the hybrid sterility between Indica and Japonica types was analyzed, and Indica, Japonica, and wide-compatibility type which gives fertile hybrids when cross to Indica and Japonica types, are proved to contain an allele, S5＇, S5＇ and S5^n, respectively at a locus on chromosome 6. And those gametes having Sj allele are found to be partially aborted in the hybrid genotypes of S5＇/S5＇ while no gamete abortion occurs in S5＇/S5^n and S5＇/S5^n genotypes. Since then, the gene S5^n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between subspecies, and the long-disputed problem of hybrid sterility has been solved. Also in such studies the characteristic association of traits found in each of vadetal groups is better explained by founder effects. On the other hand, a large number of native cultivars of rice were surveyed with enzyme polymorphism in 1980s and later with molecular markers. As a result, profound genetic diversity is found in cultivated rice as well as in wild rice. These findings seem to lead us to the idea of multiple independent domestications of rice. However, before reaching such a conclusion, at least two fa展开更多
Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies ...Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies have been conducted on genetic changes over time. In this study, we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan, Cryptomeriajaponica var. sinensis, in the Tianmushan National Nature Reserve, whose origin was debatable. The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.5999 respectively, lower than other conifers with the same life history characteristics. FST was 0.0024-0.003, and the pairwise test revealed no significant differentiation in any pair of size classes. Significant heterozygosity excesses were detected in five size classes except the oldest one, indicating bottleneck event（s）. The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.展开更多
基金financially supported by the National Key Research and Development Program of China (2017YFD0500101)the Natural Science Foundation of Jiangsu Province (BK20170721)the China Association for Science and Technology Youth Talent Lift Project (2017-2019)
文摘Since late 2011,outbreaks of pseudorabies virus(PRV)have occurred in southern China causing major economic losses to the pig industry.We previously reported that variant PRV forms and recombination in China could be the source of continued epidemics.Here,we analyzed samples from intensive pig farms in eastern China between 2017 and 2019,and sequenced the main glycoproteins(gB,gC,gD,and gE)to study the evolution characteristics of PRV.Based on the gC gene,we found that PRV variants belong to clade 2 and detected a founder effect during by the PRV epidemic.In addition,we detected inter-and intra-clade recombination;in particular,inter-clade recombination in the gB genes of strains FJ-ZXF and FJ-W2,which were recombinant with clade 1 strains.We also found specific amino-acid changes and positively selected sites,possibly associated with functional changes.This analysis of the emergence of PRV in China illustrates the need for continuous monitoring and the development of vaccines against specific variants of PRV.
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.
文摘On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps under a climate with freezing winter cold. These findings lead us to-examine the past ideas about domestication and differentiation of rice. Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Soon after that, the two types were classified by the associations of a number of genetically independent traits. The characteristic associations of traits have been explained by the hybrid sterility or reproductive barriers which were assumed to comprise a set of duplicate recessive lethal genes and to be an inner genetic mechanism to lead to the varietal differentiations In 1980s, the hybrid sterility between Indica and Japonica types was analyzed, and Indica, Japonica, and wide-compatibility type which gives fertile hybrids when cross to Indica and Japonica types, are proved to contain an allele, S5＇, S5＇ and S5^n, respectively at a locus on chromosome 6. And those gametes having Sj allele are found to be partially aborted in the hybrid genotypes of S5＇/S5＇ while no gamete abortion occurs in S5＇/S5^n and S5＇/S5^n genotypes. Since then, the gene S5^n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between subspecies, and the long-disputed problem of hybrid sterility has been solved. Also in such studies the characteristic association of traits found in each of vadetal groups is better explained by founder effects. On the other hand, a large number of native cultivars of rice were surveyed with enzyme polymorphism in 1980s and later with molecular markers. As a result, profound genetic diversity is found in cultivated rice as well as in wild rice. These findings seem to lead us to the idea of multiple independent domestications of rice. However, before reaching such a conclusion, at least two fa
基金the Program for New Century Excellent Talents in University (NCET-05-0431)funding from the Commission of Science and Technol-ogy of Lin'an City to XY Chen
文摘Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies have been conducted on genetic changes over time. In this study, we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan, Cryptomeriajaponica var. sinensis, in the Tianmushan National Nature Reserve, whose origin was debatable. The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.5999 respectively, lower than other conifers with the same life history characteristics. FST was 0.0024-0.003, and the pairwise test revealed no significant differentiation in any pair of size classes. Significant heterozygosity excesses were detected in five size classes except the oldest one, indicating bottleneck event（s）. The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.
