The Composition Vector Tree (CVTree) is a parameter-free and alignment-free method to infer pro-karyotic phylogeny from their complete genomes. It is distinct from the traditional 16S rRNA analysis in both the input d...The Composition Vector Tree (CVTree) is a parameter-free and alignment-free method to infer pro-karyotic phylogeny from their complete genomes. It is distinct from the traditional 16S rRNA analysis in both the input data and the methodology. The prokaryotic phylogenetic trees constructed by using the CVTree method agree well with the Bergey’s taxonomy in all major groupings and fine branching patterns. Thus, combined use of the CVTree approach and the 16S rRNA analysis may provide an objective and reliable reconstruction of the prokaryotic branch of the Tree of Life.展开更多
The interaction between a functionalized single-wailed carbon nanotube (f-SWCNT) and the YAP65WW protein domain is investigated by using molecular dynamics simulations.It is found that the f-SWCNT binds onto the activ...The interaction between a functionalized single-wailed carbon nanotube (f-SWCNT) and the YAP65WW protein domain is investigated by using molecular dynamics simulations.It is found that the f-SWCNT binds onto the active site of the YAP65WW domain and leads to a substantial conformational change of the protein domain,which may securely affect the original function of protein.Both the hydrophobic interaction and the long lifetime hydrogen bonds play important roles in the binding.展开更多
The behaviour of water and small solutes in confined geometries is important to a variety of chemical and nanofluidic applications. Here we investigate the permeation and distribution of water and ions in electrically...The behaviour of water and small solutes in confined geometries is important to a variety of chemical and nanofluidic applications. Here we investigate the permeation and distribution of water and ions in electrically charged carbon cylindrical nanopore during the osmotic process using molecular dynamics simulations. In the simulations, charges are distributed uniformly on the pores with diameter of 0.9 nm. For nanopores with no charge or a low charge, ions are difficult to enter. With the increasing of charge densities on the pores, ions will appear inside the nanopores because of the large electronic forces between the ions and the charged pores. Different ion entries induce varying effects on osmotic water flow. Our simulations reveal that the osmotic water can flow through the negatively charged pore occupied by K^＋ ions, while water flux through the positively charged pores will be disrupted by Cl^- ions inside the pores. This may be explained by the different radial distributions of K^＋ ions and Cl^- ions inside the charged nanopores.展开更多
Water plays an important role in the structure and function of biomolecules. Water confined at the nanoscale usually exhibits phenomena not seen in bulk water, including the ice-like ordering structure on the surfaces...Water plays an important role in the structure and function of biomolecules. Water confined at the nanoscale usually exhibits phenomena not seen in bulk water, including the ice-like ordering structure on the surfaces of many substrates. We investigate the behaviour of protein folding in which the proteins are assumed in an environment with ordering water by using of an off-lattice GO-like model, It is found that in the physiological temperature, both the folding rate and the thermodynamic stability of the protein are greatly promoted by the existence of ordering of water.展开更多
We investigate the influence of correlation between water molecules transport through the neighbouring nanopores, whose centres are at a distance of only 6.2A, using the molecular dynamics simulations. Water molecule ...We investigate the influence of correlation between water molecules transport through the neighbouring nanopores, whose centres are at a distance of only 6.2A, using the molecular dynamics simulations. Water molecule distribution in nanopore and average water flow are obtained. It is found that the average water molecule number and water flow are slightly different between a system made of the neighbouring nanopores and a system of a single pore. This indicates that transport of water chains in neighbouring pores do no show significant influence each other. These findings should be helpful in designing efficient artificial membrane made of nanopores and providing an insight into effects of the biological channel structure on the water permeation.展开更多
Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignme...Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignment-free and parameter-free CVTree approach shows convincingly that four established Shigella species, Shigella boydii, Shigella sonnei, Shigella felxneri and Shigella dysenteriae, are distinct from E. coli strains, and form sister species to E. coli within the genus Esch- erichia. In view of the overall success and high resolution power of the CVTree approach, this result should be taken seriously. We hope that the present report may promote further in-depth study of the Shigella-E. coli relationship.展开更多
Phylogenetic tree of coronaviruses (CoVs) in-cluding the human SARS-associated virus is reconstructed from complete genomes by using our newly developed K- string composition approach. The relation of the human SARS-C...Phylogenetic tree of coronaviruses (CoVs) in-cluding the human SARS-associated virus is reconstructed from complete genomes by using our newly developed K- string composition approach. The relation of the human SARS-CoV to other coronaviruses, i.e. the rooting of the tree is suggested by choosing an appropriate outgroup. SARS-CoV makes a separate group closer but still distant from G2 (CoVs in mammalian host). The relation between different isolates of the human SARS virus is inferred by first constructing an ultrametric distance matrix from counting sequence variations in the genomes. The resulting tree is consistent with clinic relations between the SARS-CoV isolates. In addition to a larger variety of coronavirus ge-nomes these results provide phylogenetic knowledge based on independent novel methodology as compared to recent phylogenetic studies on SARS-CoV.展开更多
A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference a...A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http：//tlife.fudan.edu.cn/cvtree3/without login requirements.展开更多
The newly proposed alignment-free and parameter-free composition vector (CVtree) method has been successfully applied to infer phylogenetic relationship of viruses, chloroplasts, bacteria, and fungi from their whole-g...The newly proposed alignment-free and parameter-free composition vector (CVtree) method has been successfully applied to infer phylogenetic relationship of viruses, chloroplasts, bacteria, and fungi from their whole-genome data. In this study we pay special attention to the phylogenetic positions of 56 Archaea genomes among which 7 species have not been listed either in Bergey’s Manual of Systematic Bacteriology or in Taxonomic Outline of Bacteria and Archaea (TOBA). By inspecting the stable monophyletic branchings in CVTrees reconstructed from a total of 861 genomes (56 Archaea plus 797 Bacteria, using 8 Eukarya as outgroups) definite taxonomic assignments were proposed for these not-fully-classified species. Further development of Archaea taxonomy may verify the predicted phylogenetic results of the CVTree approach.展开更多
Background： The dilemma of pathogens identification in patients with unidentified clinical symptoms such as lever of unknown origin exists, which not only poses a challenge to both the diagnostic and therapeutic proc...Background： The dilemma of pathogens identification in patients with unidentified clinical symptoms such as lever of unknown origin exists, which not only poses a challenge to both the diagnostic and therapeutic process by itself, but also to expert physicians. Methods： In this report, we have attempted to increase the awareness of unidentified pathogens by developing a method to investigate hitherto unidentified infectious pathogens based on unbiased high-throughput sequencing. Results： Our observations show that this method supplements current diagnostic technology that predominantly relies on information derived five cases from the intensive care unit. This methodological approach detects viruses and corrects the incidence of false positive detection rates of pathogens in a much shorter period. Through our method is followed by polymerase chain reaction validation, we could identify infection with Epstein-Barr virus, and in another case, we could identify infection with Streptococcus viridians based on the culture, which was false positive. Conclusions： This technology is a promising approach to revolutionize rapid diagnosis of infectious pathogens and to guide therapy that might result in the improvement of personalized medicine.展开更多
We describe an interactive viewer for the All-Species Living Tree（LVTree）. The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxo...We describe an interactive viewer for the All-Species Living Tree（LVTree）. The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16 S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner.In view of the fact that the present prokaryotic systematics is largely based on 16 S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla（Proteobacteria and Firmicutes） to monophyletic clusters.展开更多
We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacte-riologists' taxo...We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacte-riologists' taxonomy-primarily the latest online Outline of the Bergey's Manual of Systematic Bacteri-ology. The CVTree phylogeny agrees very well with the Bergey's taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences.展开更多
We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-rela...We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genomebased phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on wholegenome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.展开更多
In order to show that the newly developed K-string composition distance method, based on counting oligopeptide frequencies, for inferring phylogenetic relations of prokaryotes works equally well without requiring the ...In order to show that the newly developed K-string composition distance method, based on counting oligopeptide frequencies, for inferring phylogenetic relations of prokaryotes works equally well without requiring the whole proteome data, we used all ribosomal proteins and the set of aminoacyl tRNA synthetases for each species. The latter group has been known to yield inconsistent trees if used individually. Our trees are obtained without making any sequence alignment. Altogether 16 Archaea, 105 Bacteria and 2 Eucarya are represented on the tree. Most of the lower branchings agree well with the latest, 2003, Outline of the second edition of the Bergeys Manual of Systematic Bacteriology and the trees also suggest some relationships among higher taxa.展开更多
A long-standing question about the early evolution of club fungi(phylum Basidiomycota)is the relationship between the three major groups,Pucciniomycotina,Ustilaginomycotina and Agaricomycotina.It is unresolved whether...A long-standing question about the early evolution of club fungi(phylum Basidiomycota)is the relationship between the three major groups,Pucciniomycotina,Ustilaginomycotina and Agaricomycotina.It is unresolved whether Agaricomycotina are more closely related to Ustilaginomycotina or to Pucciniomycotina.Here we reconstructed the branching order of the three subphyla through two sources of phylogenetic signals,i.e.standard phylogenomic analysis and alignment-free phylogenetic approach.Overall,beyond congruency within the frame of standard phylogenomic analysis,our results consistently and robustly supported the early divergence of Ustilaginomycotina and a closer relationship between Agaricomycotina and Pucciniomycotina.展开更多
Composition Vector Tree(CVTree) is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It has been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and f...Composition Vector Tree(CVTree) is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It has been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplast genomes, mitochondrial genomes, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16 S r RNA sequences, we showed that CVTree software is an efficient and effective tool for studying phylogeny and taxonomy based on genome sequences. The code of CVTree software can be available at https://github.com/ghzuo/cvtree.展开更多
A monospecific genus contains a single species ever since it was proposed.Though formally more than half of the known prokaryotic genera are monospecific,we pick up those which actually raise taxonomic problems by vio...A monospecific genus contains a single species ever since it was proposed.Though formally more than half of the known prokaryotic genera are monospecific,we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it resides.Taking monophyly as a guiding principle,our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes,as provided by the LVTree Viewer and CVTree Web Server,respectively.The main purpose of this study consists in calling attention to this specific way of global taxonomic analysis.Therefore,we refrain from making formal emendations for the time being.展开更多
文摘The Composition Vector Tree (CVTree) is a parameter-free and alignment-free method to infer pro-karyotic phylogeny from their complete genomes. It is distinct from the traditional 16S rRNA analysis in both the input data and the methodology. The prokaryotic phylogenetic trees constructed by using the CVTree method agree well with the Bergey’s taxonomy in all major groupings and fine branching patterns. Thus, combined use of the CVTree approach and the 16S rRNA analysis may provide an objective and reliable reconstruction of the prokaryotic branch of the Tree of Life.
基金Supported by the Chinese Academy of Sciencesthe National Natural Science Foundation of China under Grant Nos 10825520 and 11104308.
文摘The interaction between a functionalized single-wailed carbon nanotube (f-SWCNT) and the YAP65WW protein domain is investigated by using molecular dynamics simulations.It is found that the f-SWCNT binds onto the active site of the YAP65WW domain and leads to a substantial conformational change of the protein domain,which may securely affect the original function of protein.Both the hydrophobic interaction and the long lifetime hydrogen bonds play important roles in the binding.
基金Supported by Chinese Academy of Sciences, the National Natural Science Foundation of China under Grant Nos 10604060 and 10674146, and Shanghai Supercomputer Center. We thank Professor Haiping FANG for the suggestion of the project and helpful discussion.
文摘The behaviour of water and small solutes in confined geometries is important to a variety of chemical and nanofluidic applications. Here we investigate the permeation and distribution of water and ions in electrically charged carbon cylindrical nanopore during the osmotic process using molecular dynamics simulations. In the simulations, charges are distributed uniformly on the pores with diameter of 0.9 nm. For nanopores with no charge or a low charge, ions are difficult to enter. With the increasing of charge densities on the pores, ions will appear inside the nanopores because of the large electronic forces between the ions and the charged pores. Different ion entries induce varying effects on osmotic water flow. Our simulations reveal that the osmotic water can flow through the negatively charged pore occupied by K^＋ ions, while water flux through the positively charged pores will be disrupted by Cl^- ions inside the pores. This may be explained by the different radial distributions of K^＋ ions and Cl^- ions inside the charged nanopores.
基金Supported by the National Natural Science Foundation of China under Grant Nos 10474109 and 10674146, and the Chinese Academy of Sciences.
文摘Water plays an important role in the structure and function of biomolecules. Water confined at the nanoscale usually exhibits phenomena not seen in bulk water, including the ice-like ordering structure on the surfaces of many substrates. We investigate the behaviour of protein folding in which the proteins are assumed in an environment with ordering water by using of an off-lattice GO-like model, It is found that in the physiological temperature, both the folding rate and the thermodynamic stability of the protein are greatly promoted by the existence of ordering of water.
基金Supported by Chinese Academy of Sciences, the National Natural Science Foundation of China under Grant Nos 10674146, 10604060 and 10825520, and Shanghai Supercomputer Center of China.We thank Professor Hu Jun for the suggestion of this work, and Wang Chunlei and Xiu Peng for helpful discussion and comments.
文摘We investigate the influence of correlation between water molecules transport through the neighbouring nanopores, whose centres are at a distance of only 6.2A, using the molecular dynamics simulations. Water molecule distribution in nanopore and average water flow are obtained. It is found that the average water molecule number and water flow are slightly different between a system made of the neighbouring nanopores and a system of a single pore. This indicates that transport of water chains in neighbouring pores do no show significant influence each other. These findings should be helpful in designing efficient artificial membrane made of nanopores and providing an insight into effects of the biological channel structure on the water permeation.
基金supported by the National Basic Research Program of China (973 Project, Grant No. 2007CB814800 and2013CB834100)the Shanghai Leading Academic Discipline Project (Grant No. B111)the National Key Laboratory of Applied Surface Physics and the Department of Physics, Fu-dan University
文摘Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignment-free and parameter-free CVTree approach shows convincingly that four established Shigella species, Shigella boydii, Shigella sonnei, Shigella felxneri and Shigella dysenteriae, are distinct from E. coli strains, and form sister species to E. coli within the genus Esch- erichia. In view of the overall success and high resolution power of the CVTree approach, this result should be taken seriously. We hope that the present report may promote further in-depth study of the Shigella-E. coli relationship.
文摘Phylogenetic tree of coronaviruses (CoVs) in-cluding the human SARS-associated virus is reconstructed from complete genomes by using our newly developed K- string composition approach. The relation of the human SARS-CoV to other coronaviruses, i.e. the rooting of the tree is suggested by choosing an appropriate outgroup. SARS-CoV makes a separate group closer but still distant from G2 (CoVs in mammalian host). The relation between different isolates of the human SARS virus is inferred by first constructing an ultrametric distance matrix from counting sequence variations in the genomes. The resulting tree is consistent with clinic relations between the SARS-CoV isolates. In addition to a larger variety of coronavirus ge-nomes these results provide phylogenetic knowledge based on independent novel methodology as compared to recent phylogenetic studies on SARS-CoV.
基金supported by the National Basic Research Program of the Ministry of Science and Technology of China (973 ProjectGrant No. 2013CB834100)the State Key Laboratory of Applied Surface Physics as well as the Department of Physics, Fudan University, China
文摘A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http：//tlife.fudan.edu.cn/cvtree3/without login requirements.
基金supported by the National Basic Research Program of China (2007CB814800)Shanghai Leading Academic Discipline Project (B111)
文摘The newly proposed alignment-free and parameter-free composition vector (CVtree) method has been successfully applied to infer phylogenetic relationship of viruses, chloroplasts, bacteria, and fungi from their whole-genome data. In this study we pay special attention to the phylogenetic positions of 56 Archaea genomes among which 7 species have not been listed either in Bergey’s Manual of Systematic Bacteriology or in Taxonomic Outline of Bacteria and Archaea (TOBA). By inspecting the stable monophyletic branchings in CVTrees reconstructed from a total of 861 genomes (56 Archaea plus 797 Bacteria, using 8 Eukarya as outgroups) definite taxonomic assignments were proposed for these not-fully-classified species. Further development of Archaea taxonomy may verify the predicted phylogenetic results of the CVTree approach.
文摘Background： The dilemma of pathogens identification in patients with unidentified clinical symptoms such as lever of unknown origin exists, which not only poses a challenge to both the diagnostic and therapeutic process by itself, but also to expert physicians. Methods： In this report, we have attempted to increase the awareness of unidentified pathogens by developing a method to investigate hitherto unidentified infectious pathogens based on unbiased high-throughput sequencing. Results： Our observations show that this method supplements current diagnostic technology that predominantly relies on information derived five cases from the intensive care unit. This methodological approach detects viruses and corrects the incidence of false positive detection rates of pathogens in a much shorter period. Through our method is followed by polymerase chain reaction validation, we could identify infection with Epstein-Barr virus, and in another case, we could identify infection with Streptococcus viridians based on the culture, which was false positive. Conclusions： This technology is a promising approach to revolutionize rapid diagnosis of infectious pathogens and to guide therapy that might result in the improvement of personalized medicine.
基金supported by the National Basic Research Program of China(973 ProgramGrant No.2013CB834100)
文摘We describe an interactive viewer for the All-Species Living Tree（LVTree）. The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16 S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner.In view of the fact that the present prokaryotic systematics is largely based on 16 S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla（Proteobacteria and Firmicutes） to monophyletic clusters.
文摘We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacte-riologists' taxonomy-primarily the latest online Outline of the Bergey's Manual of Systematic Bacteri-ology. The CVTree phylogeny agrees very well with the Bergey's taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences.
基金supported by the National Basic Research Program of China(973 ProjectGrant No.2013CB834100)+1 种基金the National Natural Science Foundation of China(Grant No.11474068)the support of the State Key Laboratory of Applied Surface Physics and the Department of Physics,Fudan University,China
文摘We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genomebased phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on wholegenome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.
基金This work was partly supported by the Special Funds for Major State Basic Research Projects(Grant No.G2000077308)National Natural Science Foundation of China(Grant No.30170232)+1 种基金the Innovation Project of Chinese Academy of Sciencesby a grant from Shaghai Municipality via Fudan University.
文摘In order to show that the newly developed K-string composition distance method, based on counting oligopeptide frequencies, for inferring phylogenetic relations of prokaryotes works equally well without requiring the whole proteome data, we used all ribosomal proteins and the set of aminoacyl tRNA synthetases for each species. The latter group has been known to yield inconsistent trees if used individually. Our trees are obtained without making any sequence alignment. Altogether 16 Archaea, 105 Bacteria and 2 Eucarya are represented on the tree. Most of the lower branchings agree well with the latest, 2003, Outline of the second edition of the Bergeys Manual of Systematic Bacteriology and the trees also suggest some relationships among higher taxa.
基金This work was supported by the National Basic Research Program of China(973 ProjectGrant No.2013CB834100)the National Natural Science Foundation of China(Grant No.11474068).
文摘A long-standing question about the early evolution of club fungi(phylum Basidiomycota)is the relationship between the three major groups,Pucciniomycotina,Ustilaginomycotina and Agaricomycotina.It is unresolved whether Agaricomycotina are more closely related to Ustilaginomycotina or to Pucciniomycotina.Here we reconstructed the branching order of the three subphyla through two sources of phylogenetic signals,i.e.standard phylogenomic analysis and alignment-free phylogenetic approach.Overall,beyond congruency within the frame of standard phylogenomic analysis,our results consistently and robustly supported the early divergence of Ustilaginomycotina and a closer relationship between Agaricomycotina and Pucciniomycotina.
文摘Composition Vector Tree(CVTree) is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It has been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplast genomes, mitochondrial genomes, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16 S r RNA sequences, we showed that CVTree software is an efficient and effective tool for studying phylogeny and taxonomy based on genome sequences. The code of CVTree software can be available at https://github.com/ghzuo/cvtree.
基金This work was supported by the National Basic Research Program of China(973 Project No.2013CB834100)the National Key Laboratory of Applied Surface Physics and the Department of Physics,Fudan University.
文摘A monospecific genus contains a single species ever since it was proposed.Though formally more than half of the known prokaryotic genera are monospecific,we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it resides.Taking monophyly as a guiding principle,our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes,as provided by the LVTree Viewer and CVTree Web Server,respectively.The main purpose of this study consists in calling attention to this specific way of global taxonomic analysis.Therefore,we refrain from making formal emendations for the time being.
