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Results for “phylogenetic analysis”

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PubMed2006

Phylogenetic analysis of Brazilian HIV type 1 subtype D strains: tracing the origin of this subtype in Brazil.

HIV-1 Subtype D occurs mainly in East and Central African countries, especially Uganda, where the prevalence of HIV-1 infection is among the highest in the world. We present the phylogenetic analysis of one nonautochthonous and four autochthonous (including a near full-length genome) Brazilian HIV-1 subtype D strains identified in Rio de Janeiro State, where subtypes B, F1, and BF1 recombinants predominate. Phylogenetic inferences using maximum likelihood were applied on a near-full length genome and on concatenated gag, protease, reverse transcriptase, integrase, C2V3/env, gp41, and nef segments. Sequences from an Angolan immigrant showed close genetic similarity with a strain described in Finland, from an HIV patient of African origin, whereas all four autochthonous Brazilian sequences clustered with South African strains, where subtype D occurs only in isolated cases. Our results suggest the successful introduction and circulation in Brazil of closely related HIV-1 subtype D strains, possibly of South African origin.

Brazil↗

PubMed1992

Phylogenetic analysis of the cadherin superfamily.

Cadherins are a multigene family of proteins which mediate homophilic calcium-dependent cell adhesion and are thought to play an important role in morphogenesis by mediating specific intercellular adhesion. Different lines of experimental evidence have recently indicated that the site responsible for mediating adhesive interactions is localized to the first extracellular domain of cadherin. Based upon an analysis of the sequence of this domain, I show that cadherins can be classified into three groups with distinct structural features. Furthermore, using this sequence information a phylogenetic tree relating the known cadherins was assembled. This is the first such tree to be published for the cadherins. One cadherin subtype, neural cadherin (N-cadherin), shows very little sequence divergence between species, whereas all other cadherin subtypes show more substantial divergence, suggesting that selective pressure upon this domain may be greater for N-cadherin than for other cadherins. Phylogenetic analysis also suggests that the gene duplications which established the main branches leading to the different cadherin subtypes occurred very early in their history. These duplications set the stage for the diversified superfamily we now observe.

Amino Acid Sequence↗

PubMed1993

Phylogenetic analysis of Syntrophobacter wolinii reveals a relationship with sulfate-reducing bacteria.

A 16S rRNA sequence analysis of Syntrophobacter wolinii was done by using PCR amplification of the 16S rRNA-genes from DNA isolated from the S. wolinii-Desulfovibrio sp. coculture. Phylogenetic analysis using the obtained sequence revealed that S. wolinii was not related to bacteria growing syntrophically on other fatty acids than propionate, but was related to sulfate-reducing bacteria. The closest related bacteria are Desulfomonile tiedjei and Desulfoarculus baarsii.

Base Sequence↗

PubMed2004

[Phylogenetic analysis of enterovirus 71 isolated from patients with hand, foot and mouth disease in Guangdong and Fujian provinces, 2000-2001].

OBJECTIVE: To identify enterovirus 71 (EV71) strains isolated from patients with hand, foot and mouth disease (HFMD) in Guangdong and Fujian provinces from 2000 to 2001 by using phylogenetic analysis. METHODS: All 25 samples were first tested for enteric viruses by RT-PCR using enterovirus specific primers EV-1 and EV-2, and then were identified for EV71 by RT-PCR using EV71 specific primers 159S and 162A. The amplicons of 485bp segment (part of the VP1 gene) were cloned into pGEM-T and sequenced. A phylogenetic tree was constructed by comparison of the sequences with other 12 EV71 strains isolated from China, Japan, Hungary, and the United States including the prototype BrCr. RESULTS: The positive rate of EV71 was about 20%. The sequence analysis showed that the new isolate (GZH2000) shared 94%-96% nucleotide identity with three strains isolated in 1998 and 2000, and 91% with a strain isolated in 1987 from Chinese mainland, but shared only 82%-84% homology with EV71 isolates studied abroad. CONCLUSIONS: EV71 is one of the important pathogens of HFMD in south China. The strains isolated from mainland were closely related with most isolates from Taiwan, but different from most EV71 strains reported abroad. The symptoms of EV71 infection in mainland were not as intensive as those described in Taiwan's outbreak.

Adolescent↗

PubMed1998

The expression of two engrailed-related genes in an apterygote insect and a phylogenetic analysis of insect engrailed-related genes.

Homologues of the Drosophila segment polarity gene engrailed have been cloned from many insect species, as well as other arthropods and non-arthropods. We have cloned partial cDNAs of two engrailed homologues, which we call engrailed-related genes, from the phylogenetically basal insect, Thermobia domestica (Order Thysanura) and possibly as many as four engrailed-related genes from the phylogenetically intermediate insect, Oncopeltus fasciatus (Order Hemiptera). Previous to our findings, only single engrailed-related homologues had been found in phylogenetically intermediate insect species (Tribolium and Schistocerca) and in the crustacean Artemia, while two engrailed-related homologues have been found in more derived orders (Hymenoptera and the engrailed and invected genes of lepidopterans and dipterans). Consequently, we performed a phylogenetic analysis of insect engrailed-related genes to determine whether insects ancestrally had one or two engrailed-related genes. We have found evidence of concerted evolution among engrailed-related paralogues, however, that masks the true phylogenetic history of these genes; the phylogeny may only be decipherable, therefore, by examining the presence or absence of engrailed-specific and invected-specific motifs, which will require cloning the full length cDNAs from more species. In addition, we examined the embryonic expression pattern of the two Thermobia engrailed-related genes; like Drosophila engrailed and invected, they are expressed in very similar patterns, but show one temporal difference in pregnathal segments that correlates with the tentative phylogenetic placement of the genes. Thermobia engrailed-related expression also confirms that the dorsal ridge is an ancient structure in insects.

Amino Acid Sequence↗

PubMed2004

Phylogenetic analysis of multiple loci reveal the population structure within Letharia in the Caucasus and Morocco.

The sequence variation within the genus Letharia in the Caucasus and Morocco was investigated. Twelve thalli from each area were sequenced at eight different loci. Phylogenetic analysis of the multiple loci data revealed the cryptic species Letharia 'lupina' in Morocco, previously known only from western North America. The two cryptic species L. vulpina and L. 'lupina' locally share the same ecology but are genetically isolated from each other. In the Caucasus, five different haplotypes of L. vulpina were detected, and in Morocco four L. vulpina haplotypes and six L. 'lupina' haplotypes were found. For L. vulpina, allelic differences were detected at five of the eight loci in the Caucasus and Morocco. The populations of L. vulpina in both the Caucasus and Morocco contain more genetic variation than those previously investigated in Europe, which indicates that the Caucasus and Morocco acted as refugia during quaternary glaciations, and that central and northern Europe may have been recolonised from one or both of these areas.

Alleles↗

PubMed1998

The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: a simulation study.

Many phylogenetic analyses, particularly morphological studies, use higher taxa (e.g., genera, families) rather than species as terminal taxa. This general approach requires dealing with interspecific variation among the species that make up the higher taxon. In this paper, I review different parsimony methods for coding and sampling higher taxa and compare their relative accuracies using computer simulations. Despite their widespread use, methods that involve coding higher taxa as terminals perform poorly in simulations, relative to splitting up the higher taxa and using species as terminals. Among the methods that use higher taxa as terminals, coding a taxon based on the most common condition among the included species (majority or modal coding) is generally more accurate than other coding methods, such as coding taxa as missing or polymorphic. The success of the majority method, and results of further simulations, suggest that in many cases "common equals primitive" within variable taxa, at least for low and intermediate rates of character change. The fixed-only method (excluding variable characters) performs very poorly, a result that is indirectly supported by analyses of published data for squamate reptiles. Sampling only a single species per higher taxon also yields low accuracy under many conditions. Along with recent studies of intraspecific polymorphism, the results of this study show the general importance of (1) including characters despite variation within taxa and (2) using methods that incorporate detailed information on the distribution of states within variable taxa.

Computer Simulation↗

PubMed2004

[Phylogenetic analysis of two rabies viruses, Takamen and Komatsugawa strains isolated in Japan in the 1940's].

The entire coding region of the nucleoprotein (N) gene of Takamen and Komatsugawa strains of rabies virus isolated in Japan in 1940's were determined. Phylogenetic analysis was performed on 140 lyssaviruses (128 viruses of genotype 1 and 12 lyssaviruses of other genotypes) isolated in various parts of the world, including the two Japanese rabies strains, based on the sequences of 1,350 nucleotides of the N gene. The rabies viruses were divided into 12 distinct clusters at least, reflecting geographical areas and hosts as reservoirs. The Takamen, Nishigahara, and RC-HL strains derived from the Nishigahara strain were grouped into the same cluster as the Chinese strain (3aG) in the worldwide distribution group. The Komatsugawa strain was grouped into the same cluster as the viruses from a raccoon dog from Khabarovsk, and from a steppe fox in area of Lake Baikal in Russia in a group consisting of Canada, Greenland, and the Arctic. These data along with the historical evidence suggest that Japanese rabies viruses, the Takamen and Komatsugawa strains, belong to two different clusters and moved into Japan from China and Russia, respectively.

Japan↗

PubMed2001

A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA.

The economically important plum or cherry genus (PRUNUS:) and the subfamily Amygdaloideae of the Rosaceae have a controversial taxonomic history due to the lack of a phylogenetic framework. Phylogenetic analysis using the ITS sequences of nuclear ribosomal DNA (nrDNA) was conducted to construct the evolutionary history and evaluate the historical classifications of PRUNUS: and the Amygdaloideae. The analyses suggest two major groups within the Amygdaloideae: (1) PRUNUS: s.l. (sensu lato) and MADDENIA:, and (2) EXOCHORDA:, Oemleria, and PRINSEPIA: The ITS phylogeny supports the recent treatment of including EXOCHORDA: (formerly in the Spiraeoideae) in the Amygdaloideae. MADDENIA: is found to be nested within PRUNUS: s.l. in the parsimony and distance analyses, but basal to PRUNUS: s.l. in the maximum likelihood analysis. Within PRUNUS:, two major groups are recognizable: (1) the AMYGDALUS:-PRUNUS: group, and (2) the CERASUS:-LAUROCERASUS:-PADUS: group. The clades in the ITS phylogeny are not congruent with most subgeneric groups in the widely used classification of PRUNUS: by Rehder. A broadly defined PRUNUS: is supported.

Journal Article↗

PubMed1991

Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA.

The 16S rRNA gene of the magnetotactic magnetogen Aquaspirillum magnetotacticum MS1 was amplified by a polymerase chain reaction, using two eubacterial consensus oligodeoxynucleotide primers flanking the majority of the 16S rRNA gene, cloned, and sequenced. Phylogenetic analysis revealed that A. magnetotacticum MS1 belongs to the alpha-group of proteobacteria. This assignment offers perspective on the biochemical properties of A. magnetotacticum, since this organism is expected to have the general properties that are common to this phylogenetic group.

Base Sequence↗

PubMed2003

Phylogenetic analysis and possible function of bro-like genes, a multigene family widespread among large double-stranded DNA viruses of invertebrates and bacteria.

Baculovirus repeated open reading frame (bro) genes and their relatives constitute a multigene family, typically with multiple copies per genome, known to occur among certain insect dsDNA viruses and bacteriophages. Little is known about the evolutionary history and function of the proteins encoded by these genes. Here we have shown that bro and bro-like (bro-l) genes occur among viruses of two additional invertebrate viral families, Ascoviridae and Iridoviridae, and in prokaryotic class II transposons. Analysis of over 100 sequences showed that the N-terminal region, consisting of two subdomains, is the most conserved region and contains a DNA-binding motif that has been characterized previously. Phylogenetic analysis indicated that these proteins are distributed among eight groups, Groups 1-7 consisting of invertebrate virus proteins and Group 8 of proteins in bacteriophages and bacterial transposons. No bro genes were identified in databases of invertebrate or vertebrate genomes, vertebrate viruses and transposons, nor in prokaryotic genomes, except in prophages or transposons of the latter. The phylogenetic relationship between bro genes suggests that they have resulted from recombination of viral genomes that allowed the duplication and loss of genes, but also the acquisition of genes by horizontal transfer over evolutionary time. In addition, the maintenance and diversity of bro-l genes in different types of invertebrate dsDNA viruses, but not in vertebrate viruses, suggests that these proteins play an important role in invertebrate virus biology. Experiments with the unique orf2 bro gene of Autographa californica multicapsid nucleopolyhedrovirus showed that it is not required for replication, but may enhance replication during the occlusion phase of reproduction.

Amino Acid Sequence↗

PubMed1995

Identification and phylogenetic analysis of toxigenic cyanobacteria by multiplex randomly amplified polymorphic DNA PCR.

Randomly amplified polymorphic DNA PCR was used to generate unique and identifying DNA profiles for members of the cyanobacterial genera Anabaena and Microcystis, which are responsible for much of the production of nuisance blooms in various freshwater systems, including recreational and drinking water supplies. A method based on the combination of two 10-mer oligonucleotides in a single PCR was developed to provide specific and repeatable DNA fingerprints for cyanobacterial isolates. The strain-specific randomly amplified polymorphic DNA profiles made it possible to discriminate among all toxigenic cyanobacteria studied to the three taxonomic levels of genus, species, and strain. Analysis of DNA typing results obtained by the described method clearly distinguishes between the genera Anabaena and Microcystis. The markers produced for each strain were also applied to a phylogenetic analysis to infer genetic relatedness in this group of prokaryotes.

Journal Article↗

PubMed1996

Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products.

Partial nucleotide sequences of the gyrB genes (DNA gyrase B subunit genes) of 15 Acinetobacter strains, including the type and reference strains of genomic species 1 to 12 (A. calcoaceticus [genomic species 1], A. baumannii [genomic species 2], Acinetobacter genomic species 3, A. haemolyticus [genomic species 4], A. junii [genomic species 5], Acinetobacter genomic species 6, A. johnsonii [genomic species 7], A. lwoffii [genomic species 8], Acinetobacter genomic species 9, Acinetobacter genomic species 10, Acinetobacter genomic species 11, and A. radioresistens [genomic species 12]), were determined by sequencing the PCR-amplified fragments of gyrB. The gyrB sequence homology among these Acinetobacter strains ranged from 69.6 to 99.7%. A phylogenetic analysis, using the gyrB sequences, indicates that genomic species 1, 2, and 3 formed one cluster (87.3 to 90.3% identity), while genomic species 8 and 9 formed another cluster (99.7% identity). These results are consistent with those of DNA-DNA hybridization and of biochemical systematics. On the other hand, the topology of the published phylogenetic tree based on the 16S rRNA sequences of the Acinetobacter strains was quite different from that of the gyrB-based tree. The numbers of substitution in the 16S rRNA gene sequences were not high enough to construct a reliable phylogenetic tree. The gyrB-based analysis indicates that the genus Acinetobacter is highly diverse and that a reclassification of this genus would be required.

Acinetobacter↗

PubMed2004

Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis.

Relative positions of nematodes, arthropods, and chordates in animal phylogeny remain uncertain. The traditional tree topology joins arthropods with chordates in a coelomate clade, whereas nematodes, which lack a coelome, occupy a basal position. However, the current leading hypothesis, based on phylogenetic trees for 18S ribosomal RNA and several proteins, joins nematodes with arthropods in a clade of molting animals, Ecdysozoa. We performed a phylogenetic analysis of over 500 sets of orthologous proteins, which are represented in plants, animals, and fungi, using maximum likelihood, maximum parsimony, and distance methods. Additionally, to increase the statistical power of topology tests, the same methods were applied to concatenated alignments of subunits of eight conserved macromolecular complexes. The majority of the methods, when applied to most of the orthologous clusters, both concatenated and individual, grouped the fly with humans to the exclusion of the nematode, in support of the coelomate phylogeny. Trees were also constructed using information on insertions and deletions in orthologous proteins, combinations of domains in multidomain proteins, and presence-absence of species in clusters of orthologs. All of these approaches supported the coelomate clade and showed concordance between evolution of protein sequences and higher-level evolutionary events, such as domain fusion or gene loss.

Animals↗

PubMed2005

Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors.

BACKGROUND: The cell-membrane G-protein coupled receptors (GPCRs) are one of the largest known superfamilies and are the main focus of intense pharmaceutical research due to their key role in cell physiology and disease. A large number of putative GPCRs are 'orphans' with no identified natural ligands. The first step in understanding the function of orphan GPCRs is to identify their ligands. Phylogenetic clustering methods were used to elucidate the chemical nature of receptor ligands, which led to the identification of natural ligands for many orphan receptors. We have clustered human and Drosophila receptors with known ligands and orphans through cross genome phylogenetic analysis and hypothesized higher relationship of co-clustered members that would ease ligand identification, as related receptors share ligands with similar structure or class. RESULTS: Cross-genome phylogenetic analyses were performed to identify eight major groups of GPCRs dividing them into 32 clusters of 371 human and 113 Drosophila proteins (excluding olfactory, taste and gustatory receptors) and reveal unexpected levels of evolutionary conservation across human and Drosophila GPCRs. We also observe that members of human chemokine receptors, involved in immune response, and most of nucleotide-lipid receptors (except opsins) do not have counterparts in Drosophila. Similarly, a group of Drosophila GPCRs (methuselah receptors), associated in aging, is not present in humans. CONCLUSION: Our analysis suggests ligand class association to 52 unknown Drosophila receptors and 95 unknown human GPCRs. A higher level of phylogenetic organization was revealed in which clusters with common domain architecture or cellular localization or ligand structure or chemistry or a shared function are evident across human and Drosophila genomes. Such analyses will prove valuable for identifying the natural ligands of Drosophila and human orphan receptors that can lead to a better understanding of physiological and pathological roles of these receptors.

Amino Acid Sequence↗

PubMed2005

[Molecular diversity and phylogenetic analysis of nitrogen-fixing (nifH) genes in alp prairie soil of Sanjiangyuan natural reserve].

Research on the diversity of microorganism community in natural environment has been concerned hot spot using the newly molecular biotechnology in the world now. This was the first description of the molecular diversity and phylogenetic analysis of nitrogen-fixing (nifH) genes in alp prairie soil of Sanjiangyuan natural reserve. DNA was directly extracted from the soil microorganism and amplified the nifH gene fragment using PCR by the primers of nifH-34F 5'-AAAGG(C/T)GG(A/T) ATCGG(C/T)AA(A/G) TCCACCAC-3' and nifH-491R 5'-TYGTT(G/C)GC(G/C)GC(A/G)TACAT(G/C)G CCATCAT-3'. For the gene fragment, diverse PCR products were characterized by cloning, restriction fragment length polymorphism (RFLP) analysis and sequencing. 143 clones and 35 different RFLP patterns were received in two samples by the restriction enzymes MspI and RsaI digested. ZD sample had 82 clones and 21 different RFLP patterns, and YS sample had 61 clones and 19 different RFLP patterns. There were shared 5 RFLP patterns in two samples. The analysis result found a significant dominant group of clones occurring in both samples which account for 29.3% and 32.8%, respectively, and several minor groups were also detected. 21 clones were sequenced, and their levels of nucleotide identity were from 71% to 98%. None of the sequenced nifH gene was completely identical to any deposited in the data banks, and therefore each of them belong to a noncharacterized bacterium. Finally, the phylogenetic tree was constructed by the Clustal W and Mega software. 21 sequences can be subdivided into 4 clusters in the phylogenetic tree, and most of them had the closely similar toalpha- , beta-, and gamma-Proteobacteria . The significant dominant group in YS sample and ZD sample had the closely related with Rhodobacter sphaeroides and Delftia tsuruhatensis, respectively. The YS-nifH-11 was the only sequence which had highly similar to Cyanobacteria .

Bacteria↗

PubMed1997

Phylogenetic analysis and identification of Shigella spp. by molecular probes.

Oligonucleotide probes were used for identification of Shigella and analysis of the relationship between Shigella spp. and Escherichia coli. Probe-based PCRs shown cross-reactions from Shigella to E. coli. Probe-based 16S rRNA sequencing and phylogenetic analysis showed the four species of Shigella: Sh. dysenteriae, Sh. boydii, Sh. sonnei, and Sh. flexneri, formed a cluster with E. coli. Shigella flexneri and Sh. sonnei are even more similar to E. coli than to the other two Shigella species. These results confirmed an earlier recommendation that the four species of Shigella and E. coli should be classified as five sub-groups within a single species.

DNA Probes↗

PubMed2003

Genomic and phylogenetic analysis of the S100A7 (Psoriasin) gene duplications within the region of the S100 gene cluster on human chromosome 1q21.

The human S100 gene family encodes the EF-hand superfamily of calcium-binding proteins, with at least 14 family members clustered relatively closely together on chromosome 1q21. We have analyzed the most recently available genomic sequence of the human S100 gene cluster for evidence of tandem gene duplications during primate evolutionary history. The sequences obtained from both GenBank and GoldenPath were analyzed in detail using various comparative sequence analysis tools. We found that of the S100A genes clustered relatively closely together within a genomic region of 260 kb, only the S100A7 (psoriasin) gene region showed evidence of recent duplications. The S100A7 gene duplicated region is composed of three distinct genomic regions, 33, 11, and 31 kb, respectively, that together harbor at least five identifiable S100A7-like genes. Regions 1 and 3 are in opposite orientation to each other, but each region carries two S100A7-like genes separated by an 11-kb intergenic region (region 2) that has only one S100A7-like gene, providing limited sequence resemblance to regions 1 and 3. The duplicated genomic regions 1 and 3 share a number of different retroelements including five Alu subfamily members that serve as molecular clocks. The shared (paralogous) Alu S insertions suggest that regions 1 and 3 were probably duplicated during or after the phase of AluS amplification some 30-40 mya. We used PCR to amplify an indel within intron 1 of the S100A7a and S100A7c genes that gave the same two expected product sizes using 40 human DNA samples and 1 chimpanzee sample, therefore confirming the presence of the region 1 and 3 duplication in these species. Comparative genomic analysis of the other S100 gene members shows no similarity between intergenic regions, suggesting that they diverged long before the emergence of the primates. This view was supported by the phylogenetic analysis of different human S100 proteins including the human S100A7 protein members. The S100A7 protein, also known as psoriasin, has important functions as a mediator and regulator in skin differentiation and disease (psoriasis), in breast cancer, and as a chemotactic factor for inflammatory cells. This is the first report of five copies of the S100A7 gene in the human genome, which may impact on our understanding of the possible dose effects of these genes in inflammation and normal skin development and pathogenesis.

Amino Acid Sequence↗