Based on two mitochondrial genes (cyt b, ND4) and one nuclear gene (c-mos), we explored the relationships within the Asian pit viper genus Gloydius. In total, 23 samples representing 10 species were analyzed. All phyl...Based on two mitochondrial genes (cyt b, ND4) and one nuclear gene (c-mos), we explored the relationships within the Asian pit viper genus Gloydius. In total, 23 samples representing 10 species were analyzed. All phylogenetic analyses support a monophyletic Gloydius with two major clades, one comprising G. brevicaudus, G. blomhoffii, and G. ussuriensis with the sister clade consisting of G. intermedius, G. saxatilis, G. halys and G. shedaoensis. The relationships among the three montane species G. strauchi, G. qinlingensis and G. liupanensis, as well as the two monophyletic groups, are unstable, and discussed. Divergence date estimation indicates that Gloydius lineage formed 15 Ma and diversification of the genus occurred at 9.89 Ma. Issues regarding the taxonomy of this genus are discussed where necessary.展开更多
Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under...Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes are involved. Consequently, we investigated whether or not other factors influence codon usage of coevolved genes. We used Drosophila melanogaster as a model organism. Our χ^2 test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system was significantly different （χ^2= 7945.16, P 〈 0.01）. A plot of effective number of codons against GC3s content of nuclear genes showed that few genes lie on the expected curve, indicating that codon usage was random. Correspondence analysis indicated a significant correlation between axis 1 and codon adaptation index （R = 0.947, P 〈 0.01） in every nuclear gene sequence. Thus, codon usage bias of nuclear genes appeared to be affected by translational selection. Correlation between axis 1 coordinates and GC content （R = 0.814, P 〈 0.01） indicated that the codon usage of nuclear genes was also affected by GC composition. Analysis of mitochondrial genes did not reveal a significant correlation between axis 1 and any parameter. Statistical analyses indicated that codon usages of both nDNA and mtDNA were subjected to context-dependent mutations.展开更多
The present study is in agreement with the hypothesis that the variation of ecological conditions in three rivers in northern Israel—the Dan, Hasbani and Hermon Rivers—affects the genetic variations of the species C...The present study is in agreement with the hypothesis that the variation of ecological conditions in three rivers in northern Israel—the Dan, Hasbani and Hermon Rivers—affects the genetic variations of the species Capoeta damascina. Using mitochondrial DNA (mtDNA), cytochrome b gene (Cytb), 16S and nuclear DNA (nDNA), and Random Amplified Polymorphic DNA (RAPD), four different clusters were found in the Cytb of the Hasbani and Hermon Rivers and only two in the Dan River. Moreover, the clusters in the Hasbani River differed from those found in the Hermon River. A similar result was found when an analysis was made of a different sequence from five different haplotype frequencies using the MegAlign program, the lowest being in the Dan River (only two haplotypes) and the highest in the Hasbani River (four haplotypes). The analysis of molecular variance of Cytb and 16S (AMOVA) for individuals of C. damascina from eight populations in northern Israel showed significant differences between the rivers and the populations. The analysis by mitochondrial 16S of haplotype frequencies of C. damascina populations in the rivers in northern Israel was very low compared to Ctb. Sixteen different haplotypes were found in the different rivers: eight in the Hasbani River, seven in the Dan River and only five in the Hermon River.展开更多
Dysfunctional mitochondria are implicated in various diseases,but comprehensive characterization of mitochondrial DNA(mtDNA)in the Chinese population remains limited.Here,we conducted a systematic analysis of mtDNA fr...Dysfunctional mitochondria are implicated in various diseases,but comprehensive characterization of mitochondrial DNA(mtDNA)in the Chinese population remains limited.Here,we conducted a systematic analysis of mtDNA from 7331 samples,comprising 4129 Chinese samples from the NyuWa cohort and 3202 samples from the 1000 Genomes Project(1KGP).We identified 7216 high-quality mtDNA variants,which classified 7266 samples into 22 macro-haplogroups,and detected 1466 nuclear mitochondrial DNA segments(NUMTs).Among these,88 mtDNA variants and 642 NUMTs were specific to NyuWa.Genome-wide association analyses revealed significant correlations between 12 mtDNA variants and 199 nuclear DNA(nDNA)variants.Our findings demonstrated that all individuals in both NyuWa and 1KGP harbored common NUMTs,while one-fifth possessed ultra-rare NUMTs that tended to insert into nuclear gene regions.Notably,rare NUMTs in the NyuWa cohort showed significant enrichment of nuclear breakpoints in long interspersed nuclear elements(LINEs)compared to 1KGP.Overall,this study provides the first comprehensive profile of NUMTs in the Chinese population and establishes the most extensive resource of Chinese mtDNA variants and NUMTs to date based on high-depth whole-genome sequencing,providing valuable reference resources for genetic research on mtDNA-related diseases.展开更多
基金partially funded by the National Natural Science Foundation of China(NSFC 30870290,NSFC 30970334,NSFC 31071892)the Program for New Century Excellent Talents in University(NCET-08-0908)
文摘Based on two mitochondrial genes (cyt b, ND4) and one nuclear gene (c-mos), we explored the relationships within the Asian pit viper genus Gloydius. In total, 23 samples representing 10 species were analyzed. All phylogenetic analyses support a monophyletic Gloydius with two major clades, one comprising G. brevicaudus, G. blomhoffii, and G. ussuriensis with the sister clade consisting of G. intermedius, G. saxatilis, G. halys and G. shedaoensis. The relationships among the three montane species G. strauchi, G. qinlingensis and G. liupanensis, as well as the two monophyletic groups, are unstable, and discussed. Divergence date estimation indicates that Gloydius lineage formed 15 Ma and diversification of the genus occurred at 9.89 Ma. Issues regarding the taxonomy of this genus are discussed where necessary.
基金supported by the National Natural Science Foundation of China (No.30770302 and 30570970)the Program of Ministry of Science and Technology of the Republic of China (No.2006FY110500)partially by the National Science Fund for Fostering Talents in Basic Research (NSFC-J0630964/J0109)
文摘Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes are involved. Consequently, we investigated whether or not other factors influence codon usage of coevolved genes. We used Drosophila melanogaster as a model organism. Our χ^2 test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system was significantly different （χ^2= 7945.16, P 〈 0.01）. A plot of effective number of codons against GC3s content of nuclear genes showed that few genes lie on the expected curve, indicating that codon usage was random. Correspondence analysis indicated a significant correlation between axis 1 and codon adaptation index （R = 0.947, P 〈 0.01） in every nuclear gene sequence. Thus, codon usage bias of nuclear genes appeared to be affected by translational selection. Correlation between axis 1 coordinates and GC content （R = 0.814, P 〈 0.01） indicated that the codon usage of nuclear genes was also affected by GC composition. Analysis of mitochondrial genes did not reveal a significant correlation between axis 1 and any parameter. Statistical analyses indicated that codon usages of both nDNA and mtDNA were subjected to context-dependent mutations.
文摘The present study is in agreement with the hypothesis that the variation of ecological conditions in three rivers in northern Israel—the Dan, Hasbani and Hermon Rivers—affects the genetic variations of the species Capoeta damascina. Using mitochondrial DNA (mtDNA), cytochrome b gene (Cytb), 16S and nuclear DNA (nDNA), and Random Amplified Polymorphic DNA (RAPD), four different clusters were found in the Cytb of the Hasbani and Hermon Rivers and only two in the Dan River. Moreover, the clusters in the Hasbani River differed from those found in the Hermon River. A similar result was found when an analysis was made of a different sequence from five different haplotype frequencies using the MegAlign program, the lowest being in the Dan River (only two haplotypes) and the highest in the Hasbani River (four haplotypes). The analysis of molecular variance of Cytb and 16S (AMOVA) for individuals of C. damascina from eight populations in northern Israel showed significant differences between the rivers and the populations. The analysis by mitochondrial 16S of haplotype frequencies of C. damascina populations in the rivers in northern Israel was very low compared to Ctb. Sixteen different haplotypes were found in the different rivers: eight in the Hasbani River, seven in the Dan River and only five in the Hermon River.
基金supported by the Beijing Natural Science Foundation(Grant No.L248016 to Shunmin He)the National Key R&D Program of China(Grant Nos.2021YFF0704500 to Peng Zhang and 2022YFC3400405 to Shunmin He)+2 种基金the 14th Five-year Informatization Plan of Chinese Academy of Sciences(Grant No.CAS-WX2021SF0203 to Shunmin He)the National Natural Science Foundation of China(Grant No,32470660 to Shunmin He)the China Postdoctoral Science Foundation(Grant No.2022M713311 to Yanyan Li).
文摘Dysfunctional mitochondria are implicated in various diseases,but comprehensive characterization of mitochondrial DNA(mtDNA)in the Chinese population remains limited.Here,we conducted a systematic analysis of mtDNA from 7331 samples,comprising 4129 Chinese samples from the NyuWa cohort and 3202 samples from the 1000 Genomes Project(1KGP).We identified 7216 high-quality mtDNA variants,which classified 7266 samples into 22 macro-haplogroups,and detected 1466 nuclear mitochondrial DNA segments(NUMTs).Among these,88 mtDNA variants and 642 NUMTs were specific to NyuWa.Genome-wide association analyses revealed significant correlations between 12 mtDNA variants and 199 nuclear DNA(nDNA)variants.Our findings demonstrated that all individuals in both NyuWa and 1KGP harbored common NUMTs,while one-fifth possessed ultra-rare NUMTs that tended to insert into nuclear gene regions.Notably,rare NUMTs in the NyuWa cohort showed significant enrichment of nuclear breakpoints in long interspersed nuclear elements(LINEs)compared to 1KGP.Overall,this study provides the first comprehensive profile of NUMTs in the Chinese population and establishes the most extensive resource of Chinese mtDNA variants and NUMTs to date based on high-depth whole-genome sequencing,providing valuable reference resources for genetic research on mtDNA-related diseases.
