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At least 19 recordsLinked to original sources
PubMed1992

DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules.

DNA Translator and Aligner are molecular phylogenetics HyperCard stacks for Macintosh computers. They manipulate sequence data to provide graphical gene mapping, conversions, translations and manual multiple-sequence alignment editing. DNA Translator is able to convert documented GenBank or EMBL documented sequences into linearized, rescalable gene maps whose gene sequences are extractable by clicking on the corresponding map button or by selection from a scrolling list. Provided gene maps, complete with extractable sequences, consist of nine metazoan, one yeast, and one ciliate mitochondrial DNAs and three green plant chloroplast DNAs. Single or multiple sequences can be manipulated to aid in phylogenetic analysis. Sequences can be translated between nucleic acids and proteins in either direction with flexible support of alternate genetic codes and ambiguous nucleotide symbols. Multiple aligned sequence output from diverse sources can be converted to Nexus, Hennig86 or PHYLIP format for subsequent phylogenetic analysis. Input or output alignments can be examined with Aligner, a convenient accessory stack included in the DNA Translator package. Aligner is an editor for the manual alignment of up to 100 sequences that toggles between display of matched characters and normal unmatched sequences. DNA Translator also generates graphic displays of amino acid coding and codon usage frequency relative to all other, or only synonymous, codons for approximately 70 select organism-organelle combinations. Codon usage data is compatible with spreadsheet or UWGCG formats for incorporation of additional molecules of interest. The complete package is available via anonymous ftp and is free for non-commercial uses.

Amino Acid Sequence↗
PubMed2026

Molecular epidemiology and phylogenetic analysis of Anaplasma ovis and Anaplasma marginale in Ixodidae infesting livestock in northwestern Iran.

BACKGROUND: Anaplasma marginale and Anaplasma ovis are tick-borne obligate intracellular bacteria causing anaplasmosis in cattle and small ruminants, respectively, with considerable economic losses worldwide. Given the favorable ecological conditions for tick survival and the limitation of data on Anaplasma spp. in local tick populations in northwestern Iran, this study aimed to molecular and phylogenetic analysis of A. ovis and A. marginale in Ixodidae infesting livestock in northwestern Iran. METHODS: In this cross-sectional study, a total of 780 ixodid ticks were collected from livestock across 198 herds in 11 counties of Ardabil Province during 2025. Ticks were morphologically identified and grouped into pools based on species and host type. Genomic DNA was extracted using a commercial kit and molecular detection of A. ovis and A. marginale was performed using PCR assays targeting the 16&#xa0;S rRNA and groEL genes. Positive samples were submitted for Sanger sequencing to confirm the identity of Anaplasma spp., phylogenetic analysis was conducted using reference sequences from GenBank (NCBI) using MEGA software (version 12). Statistical analyses were conducted using SPSS (version 25), and associations between categorical variables were assessed using Fisher's exact test (p < 0.05). RESULTS: Eight tick species belonging to three genera were identified. Among the hosts, sheep exhibited the highest infestation rate (49.3%). Hyalomma anatolicum anatolicum was the most prevalent species (25.3%) and was present in all sampled counties. Tick distribution varied significantly among host species (p = 0.003) and geographic locations (p = 0.002). PCR analysis detected A. ovis DNA in 16.6% (4/24) and A. marginale DNA in 8.3% (2/24) of tick pools. Positive pools were primarily associated with Rhipicephalus spp. and Dermacentor marginatus. According to the results of the statistical analysis a significant association was found between tick species and host type (&#x3c7;&#xb2; = 13.87, p = 0.0031), with Hyalomma anatolicum anatolicum more prevalent in sheep (p = 0.001). Tick abundance varied across counties (&#x3c7;&#xb2; = 16.42, p = 0.002), with highest densities in Nir, Khalkhal, and Kowsar (&#x3c7;&#xb2; = 14.21, p = 0.0028). No significant association was observed between Anaplasma positivity and tick species (p = 0.21) or host type (p = 0.09). CONCLUSIONS: The detection of A. ovis and A. marginale DNA in ixodid tick pools indicates their circulation in Ardabil Province. However, due to pooled sampling and the limited number of positive samples, the infection rate at the individual tick level could not be determined. These findings also highlight the importance of a One Health approach, considering the interconnected roles of animal health, tick vectors, and the environment in the transmission and control of tick-borne diseases.

Animals↗
PubMed1989

[Phylogenetic analysis of genes of the influenza virus. Relationship between adaptability and neutrality].

Detailed phylogenetic analysis of the gene family of hemagglutinin H3 of influenza A-type virus was fulfilled, taking into account the domain structure of protein and positions of antigen determinants. The densities of distribution of fixed synonimic replacements between domains HA1 and HA2 were shown to be actually equal (rho (HA1) = rho (HA2], and those of nonsynonimic ones to be unequal: their ratios were rho (HA1): rho (HA2) = 2.8 for nonepidemic branches, and rho (HA1): rho (HA2) = 7.7 for epidemic ones. For the positions of antigen determinants (agd) these densities differ still stronger from HA2: rho (agd): rho (HA2) = 10 for nonepidemic branches, and rho (agd): rho (HA2) = 36 for epidemic ones. In total, the rate of fixation of nonsynonimic replacements per position of antigen determinants for epidemic branches is 32 times higher than for nonepidemic ones. The absolute value of this estimation is K(ns)d = (9.1 +/- 0.7).10(-3) of nonsynonimic replacements per nonsynonimic position per year and seems to be twice as much as the maximum rate of neutral fixations Ks = (4.28 +/- 0.68).10(-3). Therefore, the epidemic reproduction of influenza virus is highly adaptive, exactly being focused on positions of antigen determinants. The evolution of influenza virus is stochastic process, both with the neutral and adaptive fixations.

Genes, Viral↗
PubMed1989

[A phylogenetic analysis of genes of the influenza virus. Phylogenetic trees and fixation rates].

The phylogenetic trees of influenza virus genes of hemagglutinins, neuraminidases, and of NS genes were composed. Considering properties of synonimic replacements to be neutral and their rates constant at each tree, the dates of ancestor branch points were calculated, and the rates of fixation of synonimic (Ks) and non-synonimic (Kns) replacements estimated. The epidemic branches were mostly shown to be "deadlocks", non-epidemic ones being internal or "roots." The ratios of the numbers of synonimic to non-synonimic replacements (vs/vns) were correspondingly 1.32+/-0.42 and 4.78+/-1.28 for all trees, the difference being significant. It was shown that the dated branch points for hemagglutinins are non-randomly clustered around the initial points of the main genetic shifts of the A-type virus, corresponding to the influenza pandemics. It seems that these ancestor forms of virus behave similar to the "train" of these shifts, reproducing together with the pandemic forms under conditions of decreased immune resistance of host population. The rates of fixation of non-synonimic replacements in the epidemic branches of this tree are 4 times increased, as compared to non-epidemic ones.

Genes, Viral↗
PubMed1991

The use of serological differentiation indices for the phylogenetic analysis of plant virus relationships.

The potential use of serological differentiation indices (SDIs) in the phylogenetic analysis of plant virus coat protein relationships is presented. Relationship dendrograms were constructed from SDI data for viruses in the tymovirus and Subgroup I geminivirus taxonomic groups, using distance or phenetic methods embodied in the computer programmes FITCH and NJTREE. Relationship dendrograms for geminiviruses agreed well with those constructed by others from sequence or other data; the dendrogram for tymoviruses was not in agreement with one calculated from amino acid composition data, or from other properties, but appears consistent with recently-shown sequence similarities between tymoviruses. Implications of these results for the classification and taxonomy of plant viruses are discussed.

Data Interpretation, Statistical↗
PubMed1992

Phylogenetic analysis of the genera Planococcus, Marinococcus and Sporosarcina and their relationships to members of the genus Bacillus.

A phylogenetic analysis based on 16S rRNA was performed on the genera Planococcus, Marinococcus, Sporosarcina and endospore-forming rods. In agreement with earlier 16S rRNA cataloguing data, Planococcus citreus and Sporosarcina ureae clustered with Bacillus pasteurii and other bacilli containing lysine in their cell walls. Sporosarcina halophila was shown to be genetically distinct from S. ureae and formed a loose association with the main Bacillus subtilis grouping. Marinococcus halophilus (formerly Planococcus halophilus) exhibited low levels of relatedness to all reference species examined and formed a distinct line of descent.

Bacillaceae↗
PubMed1986

Genomic blot hybridization as a tool of phylogenetic analysis: evolutionary divergence in the genus Drosophila.

Comparative, quantitative Southern analysis of genomic DNA, using single-copy sequence probes, potentially is valuable for phylogenetic analysis. We have examined 27 Drosophila species, belonging to two subgenera, seven species groups, and ten subgroups, using a variety of cloned and characterized probes: twelve cloned sequences from D. melanogaster, two from D. pseudoobscura, and two from D. grimshawi. The data are generally congruent with accepted phylogenetic relationships in Drosophila, and confirm or clarify some previously uncertain relationships. The potential and limitations of the method are discussed.

Animals↗
PubMed1989

Phylogenetic analysis of the class Sporozoea (phylum Apicomplexa Levine, 1970): evidence for the independent evolution of heteroxenous life cycles.

A phylogenetic analysis of representative genera in the class Sporozoea was undertaken using biological and morphological features to infer evolutionary relationships among the widely recognized groups in the class. Gregarines were used as a functional outgroup to the remaining sporozoa (adeleids, eimeriorins, haemosporinids, and piroplasms). The piroplasms were shown to be closely related to the adeleid parasites. Species of Babesia and Theileria were shown not to form a sister group to the haemosporinids as has been frequently suggested. The data indicate that the biologically diverse family Haemogregarinidae should be divided into at least 3 families (Haemogregarinidae Neveu-Lemaire, 1901, containing the genera Haemogregarina and Cyrilia; Karyolysidae Wenyon, 1926, containing the genus Karyolysus; Hepatozoidae Wenyon, 1926, containing the genus Hepatozoon) because the 4 genera currently within the family do not form a monophyletic group. Correlation between parasite phylogeny and taxonomic affinities of their definitive hosts suggests that the definitive hosts of heteroxenous sporozoa are their ancestral hosts. Heteroxenous sporozoan life cycles apparently have evolved independently to adapt to changes in the feeding behaviors of their definitive hosts.

Animals↗
PubMed1992

Phylogenetic analysis of alphaviruses in the Venezuelan equine encephalitis complex and identification of the source of epizootic viruses.

We studied the evolution of alphaviruses in the Venezuelan equine encephalitis (VEE) complex using phylogenetic analysis of RNA nucleotide sequences from limited portions of the nsP4, E1, and 3' untranslated genome regions of representative strains. The VEE complex constituted a monophyletic group of viruses (descended from a common ancestor); some serologic VEE varieties such as subtype III formed monophyletic groups while subtype I did not. Subtype II Everglades and variety ID enzootic viruses formed a monophyletic group which also included all epizootic variety IAB and IC VEE isolates. Everglades virus diverged from this ID lineage (colonized North America) ca. 100-150 years ago, followed by divergence of variety IAB and IC epizootic viruses. Variety IAB viruses probably emerged from the variety ID lineage once during the early part of this century, while variety IC viruses evolved at least two times. These results identify the source of epizootic VEE viruses as the variety ID enzootic virus lineage which occurs in northern South America and Panama. Even if variety IAB and IC viruses are extinct, recent, multiple emergences of epizootic viruses from an enzootic lineage suggests that other epizootic VEE viruses may evolve again in the future. The close genetic relationship of subtype II Everglades virus to the variety ID lineage also implies the potential for emergence of equine-virulent VEE viruses in Florida.

Base Sequence↗
PubMedDate not supplied

Phylogenetic analysis of the Diplomonadida (Wenyon, 1926) Brugerolle, 1975: evidence for heterochrony in protozoa and against Giardia lamblia as a "missing link".

A suite of 23 ultrastructural characters was used in a phylogenetic analysis of the protozoan order Diplomonadida. A single most parsimonious solution was found, with a length of 38 transformations and a consistency index of 0.84. The cladogram supports previous hypotheses of the relationships of the genera in the suborder Diplomonadina, as well as the inclusion of the genera Enteromonas and Trimitus in the order. Heterochrony is suggested in the change to binary axial symmetry, as hypermorphosis resulting from delayed cytokinesis in the ancestor. Hypotheses regarding a pivotal position for Giardia lamblia in the evolution of eukaryotes are inconsistent with the phylogeny proposed here.

Animals↗
PubMed1990

Phylogenetic analysis and secondary structure of the Bacillus subtilis bacteriophage RNA required for DNA packaging.

An unusual RNA molecule encoded by the Bacillus subtilis bacteriophage phi 29 is a structural component of the viral prohead and is required for the ATP-dependent packaging of DNA. Here we report a model of secondary structure for this prohead RNA developed from a phylogenetic analysis of the primary sequences of prohead RNAs of related phages. Twenty-nine phages related to phi 29 were found to produce prohead RNAs. These RNAs were analyzed by their ability to replace phi 29 RNA in in vitro phage assembly, by Northern blot hybridization with a probe complementary to phi 29 RNA, and by partial and complete sequence analyses. These analyses revealed four quite different sequences ranging in length from 161 to 174 residues. The secondary structure deduced from these sequences, in agreement with earlier observations, indicated that prohead RNA is organized into two domains. The larger 5'-domain (Domain I) is composed of 113-117 residues and contains four helices. Three of these helices appear to be organized into a central stem that is interrupted by two unpaired loops and the fourth helix and loop. The smaller 3'-domain (Domain II) is composed of 40-44 residues and consists of two helices. Domains I and II are separated by 8-13 unpaired residues. Nuclease cleavage occurs readily in this single-stranded joining region, and this cleavage allows the subsequent separation of the two RNA domains. The separated Domain I is fully active in DNA packaging in vitro. The functional significance and biological role of Domain II are unknown. The phylogenetic secondary structure model provides a basis for further analysis of the role of this RNA in bacteriophage morphogenesis.

Bacillus subtilis↗
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↗
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↗
PubMed1992

Small subunit ribosomal RNA of Blastomyces dermatitidis: sequence and phylogenetic analysis.

We determined the small subunit (18S) ribosomal RNA sequence of the dimorphic fungus Blastomyces dermatitidis. The sequence was compared to that of fourteen other eukaryotic organisms, ten of which were higher fungi, and an evolutionary tree was constructed based on these sequences. B. dermatitidis aligned most closely with the Ascomycetes Neurospora crassa and Podospora anserina, in agreement with previous phylogenetic analysis based on morphological criteria. Phase-specific cDNA clones derived by reverse transcription of RNA isolated from the yeast and mycelial phases of B. dermatitidis were also sequenced. The 18S ribosome sequence was found to be the same in both phases. Heterogeneity was found at both the genomic and RNA level at position 1352.

Base Sequence↗
PubMed1992

Phylogenetic analysis of the thiolase family. Implications for the evolutionary origin of peroxisomes.

The thiolase family is a widespread group of proteins present in prokaryotes and three cellular compartments of eukaryotes. This fact makes this family interesting in order to study the evolutionary process of eukaryotes. Using the sequence of peroxisomal thiolase from Saccharomyces cerevisiae recently obtained by us and the other known thiolase sequences, a phylogenetic analysis has been carried out. It shows that all these proteins derived from a primitive enzyme, present in the common ancestor of eubacteria and eukaryotes, which evolved into different specialized thiolases confined to various cell compartments. The evolutionary tree obtained is compatible with the endosymbiotic theory for the origin of peroxisomes.

Acetyl-CoA C-Acetyltransferase↗
PubMed1991

Structural and phylogenetic analysis of the chicken ventricular myosin heavy chain rod.

We have isolated and characterized five overlapping clones that encompass 3.2 kb and encode a part of the short subfragment 2, the hinge, and the light meromyosin regions of the myosin heavy chain rod as well as 143 bp of the 3' untranslated portion of the mRNA. Northern blot analysis showed expression of this mRNA mainly in ventricular muscle of the adult chicken heart, with trace levels detected in the atrium. Transient expression was seen in skeletal muscle during development and in regenerating skeletal muscle following freeze injury. To our knowledge, this is the first report of an avian ventricular myosin heavy chain sequence. Phylogenetic analysis indicated that this isoform is a distant homolog of other ventricular and skeletal muscle myosin heavy chains and represents a distinct member of the multigene family of sarcomeric myosin heavy chains. The ventricular myosin heavy chain of the chicken is either paralogous to its counterpart in other vertebrates or has diverged at a significantly higher rate.

Amino Acid Sequence↗
PubMed2026

The complete chloroplast genome sequence and phylogenetic analysis of Amorphophallus gigas.

We sequenced the complete chloroplast genome of Amorphophallus gigas, a perennial monocotyledonous herb in Araceae, using HiFi technology. The genome is 173,034 bp in length with a GC content of 34.96%. It exhibits a typical quadripartite structure: a large single-copy (LSC) region of 95,283 bp, a small single-copy (SSC) region of 15,675 bp, and a pair of inverted repeat (IR) regions of 31,038 bp each. It encodes 130 genes (85 protein-coding, 37 tRNA, 8 rRNA). Phylogenetic analysis revealed that A. gigas is closely related to A. titanum, forming a distinct clade. This study provides valuable genomic resources for understanding the evolution of Amorphophallus and Araceae.

Complete chloroplast genome↗