The adaptive evolution of the rbcL gene in 14 species of Ephedra and 9 other gymnosperms was tested by the PAML program. Three large-scale selections were found in the catalytic region of the RbcL protein by branch mo...The adaptive evolution of the rbcL gene in 14 species of Ephedra and 9 other gymnosperms was tested by the PAML program. Three large-scale selections were found in the catalytic region of the RbcL protein by branch model. Species in Ephedra with positive selection at the 365th codon site in rbcL gene were detected by branch-site model. 3D structure modeling showed that the 365th codon could change the spatial structure of the β-sheet (βG, βH, or βE) of the RbcL protein. These changes may be associated with the adaptation of the protein in Ephedra to the environment.展开更多
Arabidopsis thaliana(A.thaliana)has long been a model species for dicotyledon study,and was the first flowering plant to get its genome completed sequenced[1].Although most wild A.thaliana are collected in Europe,seve...Arabidopsis thaliana(A.thaliana)has long been a model species for dicotyledon study,and was the first flowering plant to get its genome completed sequenced[1].Although most wild A.thaliana are collected in Europe,several studies have found a rapid A.thaliana west-east expansion from Central Asia[2].The Qinghai-Tibet Plateau(QTP)is close to Central Asia and known for its high alti-展开更多
An updated collection of 791 human hepatitis B virus (HBV) genomes and 38 non-human primate HBV genomes was analyzed for identifying putative recombination events and their recombinants by using two bioinformatics sof...An updated collection of 791 human hepatitis B virus (HBV) genomes and 38 non-human primate HBV genomes was analyzed for identifying putative recombination events and their recombinants by using two bioinformatics software tools: Simplot and RDP3 with five algorithms (RDP, GENECONV, MaxChi, Chimaera, and SiScan). A total of 61 recombinants from nine putative recombination events were detected with RDP3, especially the breakpoints of six events which have both two parental sequences that can be determined precisely with Simplot. To our knowledge, 53 recombinants were found for the first time. Our study also suggests that a relatively high recombination frequency occurs in the PreC/C gene region and the position near gene boundaries.展开更多
基金supported by National Infrastructure of Natural Resources for Science and Technology (2005DKA21403)MOST Basic Science and Technology (2007FY110100)+2 种基金Shanghai Leading Academic Discipline Project (B111)National Science Fund for Fostering Talents in Basic Science (J0630643)the Graduate Students Innovation Foundation of Fudan University (EYH1322098)
文摘The adaptive evolution of the rbcL gene in 14 species of Ephedra and 9 other gymnosperms was tested by the PAML program. Three large-scale selections were found in the catalytic region of the RbcL protein by branch model. Species in Ephedra with positive selection at the 365th codon site in rbcL gene were detected by branch-site model. 3D structure modeling showed that the 365th codon could change the spatial structure of the β-sheet (βG, βH, or βE) of the RbcL protein. These changes may be associated with the adaptation of the protein in Ephedra to the environment.
基金supported by the National Natural Science Foundation of China (91131901)the specimen platform of China (teaching specimens sub-platform) and PSCIRT project
文摘Arabidopsis thaliana(A.thaliana)has long been a model species for dicotyledon study,and was the first flowering plant to get its genome completed sequenced[1].Although most wild A.thaliana are collected in Europe,several studies have found a rapid A.thaliana west-east expansion from Central Asia[2].The Qinghai-Tibet Plateau(QTP)is close to Central Asia and known for its high alti-
基金supported by Shanghai Leading Academic Discipline Project (B111)Shanghai Science and Technology Committee (07XD14025)
文摘An updated collection of 791 human hepatitis B virus (HBV) genomes and 38 non-human primate HBV genomes was analyzed for identifying putative recombination events and their recombinants by using two bioinformatics software tools: Simplot and RDP3 with five algorithms (RDP, GENECONV, MaxChi, Chimaera, and SiScan). A total of 61 recombinants from nine putative recombination events were detected with RDP3, especially the breakpoints of six events which have both two parental sequences that can be determined precisely with Simplot. To our knowledge, 53 recombinants were found for the first time. Our study also suggests that a relatively high recombination frequency occurs in the PreC/C gene region and the position near gene boundaries.
