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PubMed2003

Phylogenetic analysis of the first complete hepatitis E virus (HEV) genome from Africa.

Hepatitis E virus (HEV) is globally distributed, transmitted enterically and between humans and animals. Phylogenetic analysis has identified five distinct HEV genotypes. The first full-length sequence of an African strain (Chad) is presented and compared to 31 complete HEV genomes available, including the fulminant hepatitis strain from India, swine strains and a strain from Morocco. The two African strains are more closely related to genotype 1 than to any other genotypes and together they possibly form a sub-genotype or sixth genotype. The first evidence for recombination between divergent HEV strains is presented.

Chad↗

PubMed1980

Phylogenetic analysis of the mycoplasmas.

The phylogenetic relationships between the mycoplasmas and bacteria have been established from a comparative analysis of their 16S rRNA oligonucleotide catalogs. The genera Mycoplasma, Spiroplasma, and Acholeplasma arose by degenerative evolution, as a deep branch of the subline of clostridial ancestry that led to Bacillus and Lactobacillus. Thermoplasma has no specific relationship to the other mycoplasmas; it belongs with the archaebacteria.

Acholeplasma↗

PubMed2003

Phylogenetic analysis of rubella virus isolated during a period of epidemic transmission in Italy, 1991-1997.

To study the molecular epidemiology of rubella virus during endemic transmission, phylogenetic analysis of the nucleotide sequence of the E1 gene was done with 31 isolates collected in northern Italy during 1991-1997, a period spanning 3 epidemics. The viruses segregated into distinct genotypic strains. Cocirculation of genotypic strains was detected; however, each epidemic was associated with specific strains, and strain displacement occurred concomitantly with each epidemic. Although most of the viruses from Italy belonged to rubella genotype I and many were related to viruses isolated concurrently in other European countries, 3 viruses belonged to rubella genotype II, which previously had been isolated only in Asia. Thus, intercontinental importation of viruses also occurred.

Adult↗

PubMed2003

Alignment and phylogenetic analysis of beta-fibrinogen intron 7 sequences among avian orders reveal conserved regions within the intron.

We sequenced beta-fibrinogen intron 7 (beta-fibint 7) from 28 species of birds, representing 18 families in nine orders. Although the antiquity of the avian orders is estimated to be 55 to 90 Myr, and numerous indels have accrued among diverging lineages, the intron sequences were not difficult to align. However, alignment of avian sequences with mammal or snake sequences was difficult, and the residual phylogenetic signal was weak. beta-fibint 7 is an AT-rich intron, and its base composition varies little over the diversity of birds represented by our sample. Alignment of these anciently diverged sequences reveals at least five clusters of conserved nucleotides; at least two clusters appear to be in excess of the minimal set usually associated with intron excision, but their functions are unknown. Two equally most-parsimonious (MP) trees were found when indels were not included in the phylogenetic analysis, and six such trees were found when indels were included. The Neighbor-Joining and maximum-likelihood trees were identical to each other and to one of the MP trees in each MP analysis. Indels, as well as nucleotide substitutions, are phylogenetically informative, and bootstrap support exceeded 90% for 21 of 24 inferred nodes when indels were included in the MP analysis. All traditional orders represented by two or more species appear monophyletic. Relationships among avian orders are strongly supported with the exception of an inferred sister-group relationship between Caprimulgiformes and Columbiformes. A relatively close relationship between Piciformes and Passeriformes is inferred, at odds with earlier DNA-DNA hybridization studies but consistent with traditional classifications. Among Passeriformes, the traditional perspective of a sister-group relationship of suboscines and oscines is supported, as is the subsequent split of the oscines into a lineage representative of the Corvida before the diversification of the Passerida. The four species of owls divide into two strongly supported clades, corresponding to the widely accepted bifurcation of owls into two families, Tytonidae and Strigidae. A sister-group relationship between gallinaceous birds and waterfowl, the Galloanserae, is also strongly supported.

Animals↗

PubMed1995

Phylogenetic analysis of the mitochondrial genomes from Leber hereditary optic neuropathy pedigrees.

The nucleotide sequences of the mitochondrial genomes from patients with Leber hereditary optic neuropathy (LHON) were used for phylogenetic analysis to study the origin and population history of pathogenic mitochondrial mutations. Sequences of both the coding region (8300 bp) and the more rapidly evolving noncoding control region (1300 bp) were analyzed. Patients with the primary LHON mutations at nucleotides 3460, 11,778, and 14,484 were included in this study, as were LHON patients and non-LHON controls that lacked these primary mutations; some of the subjects also carried secondary LHON mutations. The phylogenetic analyses demonstrate that primary LHON mutations arose and were fixed multiple times within the population, even for the small set of LHON patients that was analyzed in these initial studies. In contrast, the secondary LHON mutations at nucleotides 4216, 4917, and 13,708 arose once: the mitochondrial genomes that carried these secondary mutations formed a well-supported phylogenetic cluster that apparently arose 60,000 to 100,000 years ago. Previous studies found secondary LHON mutations at a higher frequency among LHON patients than among control subjects. However, this finding does not prove a pathogenetic role of these mutations in LHON. Instead, the increased frequency is more likely to reflect the population genetic history of secondary mutations relative to that of primary LHON mutations.

Animals↗

PubMed1998

Phylogenetic analysis of southern hemisphere flat oysters based on partial mitochondrial 16S rDNA gene sequences.

Oysters are among the most familiar, best studied, and morphologically variable of all marine invertebrate taxa. However, our knowledge of oyster phylogeny and systematics is rudimentary, especially for the subfamily Ostreinae (flat oysters). It is unclear, for instance, whether the predominant flat oysters occurring between latitudes 35 and 50 degrees S constitute a single circumglobal species, or multiple, phylogenetically distinct, regional taxa. We have performed the first DNA molecular phylogenetic analysis of ostreinid taxa to distinguish among competing phylogenetic and systematic hypotheses for Southern Hemisphere Ostreinae. An approximately 450-nucleotide fragment of the mitochondrial large ribosomal subunit (16S) was sequenced for 41 individual oysters, representing 14 taxa of brooding oysters: 5 Southern Hemisphere Ostreinae, 5 Northern Hemisphere Ostreinae, and 4 outgroup species of the subfamily Lophinae. Phylogenetic analyses of the resulting data set yielded consensus tree topologies that are comprehensively incongruent with prevailing morphologically based interpretations of systematic relationships among the Ostreinae. Three ostreinid mitochondrial clades were evident, each containing representatives of Southern Hemisphere regional ostreinid taxa, some of which robustly cocluster with Northern Hemisphere taxa. These three clades represent the first well-supported phylogenetic framework for this ecologically prominent and commercially important oyster subfamily.

Animals↗

PubMed1998

Characterization and phylogenetic analysis of a cDNA encoding the Fes/FER related, non-receptor protein-tyrosine kinase in the marine sponge sycon raphanus.

In search of ancient versions of phylogenetically conserved genes/proteins, which are typical for multicellular animals, we have decided to analyse marine sponges (Porifera), the most ancient and most primitive metazoan organisms. We report here the complete nucleotide sequence of Sycon raphanus cDNA coding for a 879 aa long protein, which displays high overall similarity in primary structure and organization of domains with non-receptor tyrosine kinases (TKs) from the Fes/FER family. The encoded protein, which we named Fes/FER_SR, has a highly conserved, 260 aa long tyrosine kinase domain at the C-terminus. Amino-terminal to the catalytic domain is an 85 aa long SH2 domain. The N-terminus is over 500 aa long and displays homology only with N-terminal domains of protein-tyrosine kinases (PTKs) from the Fes/FER family. Mammalian Fes/FER proteins show around 58% overall homology with Fes/FER_SR (identity and similarity) and lower homology was found with Drosophila melanogaster Fps (FER) protein (49%). Homologies in TK, SH2 and N-terminal domains are on average 78%, 65% and 49%, respectively. Fes/FER_SR shows next to best homology with the Abl family of non-receptor PTKs, while Src-related PTKs from the fresh-water sponge Spongilla lacustris are related only distantly to Fes/FER_SR. Phylogenetic analysis shows that the S. raphanus TK is indeed the most ancient known member of the Fes/FER family of non-receptor PTKs. The role of these PTKs in signal transduction in higher animals is still enigmatic; they are present in the nucleus as well as in the cytoplasm and FER is found in all cell types examined. The function of Fes/FER_SR in sponge, the most primitive multicellular animal which lacks specialized organ systems, remains to be elucidated.

Amino Acid Sequence↗

PubMed2000

Identification of a new HIV-2 subtype based on phylogenetic analysis of full-length genomic sequence.

Human immunodeficiency virus type 2 (HIV-2) and simian immunodeficiency virus from sooty mangabey (SIV(SM) form one of the six primate lentivirus lineages. The close phylogenetic relationship and geographic coincidence indicate that HIV-2 originated from cross-species transmission of SIV(SM) to humans. HIV-2 exhibits considerable genetic diversity, with subtypes A-F identified. Previously, we reported the partial gag and env sequences of an unusual HIV-2 isolate, Abt96. Abt96 was collected in Ivory Coast from an asymptomatic blood donor. Here we describe the near full-length genomic sequence of Abt96. The genome was assembled from overlapping PCR fragments amplified from viral RNA isolated from plasma. Phylogenetic analysis of sequences derived from segments of the Abt96 genome demonstrate that the Abt96 isolate branches independently of all other characterized HIV-2 isolates. On the basis of the phylogenetic data being presented, we propose that Abt96 is a new HIV-2 subtype and designate it subtype G.

Animals↗

PubMed2003

Phylogenetic analysis of new plant myosin sequences.

We have sampled a large number of plant taxa, ranging from brown algae to angiosperms, for the presence of myosin sequences. Using phylogenetic analysis, we show that all but two of the new plant myosin sequences fall into two of three preexisting myosin classes. We identified two outlying sequences, which do not fall into any preexisting myosin class. Additionally, all genomic sequences encoding class XI myosins contain an intron in the region studied, suggesting that this genomic region has been conserved over at least 1 billion years of plant evolution. With these data, we can rapidly and consistently classify partial myosin sequences from plants. Our data show that plant myosins do not have clear orthologues in other kingdoms, providing interesting insights into the diversification of myosins.

Evolution, Molecular↗

PubMed1995

Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents.

We analyze sequences from two mitochondrial genes, cytochrome b (cyt b) and 12S rRNA (12S), for a group of sigmodontine rodents among which phylogenetic relationships are well understood based on concordance of morphological, chromosomal, allozyme, and other DNA data sets. Because these two genes are physically linked on the nonrecombining mitochondrial genome, they necessarily share the same history. Phylogenetic analysis of the cyt b gene recovers the well-corroborated relationships, generally with strong support. None of the methods that we employed, including variously weighted parsimony, neighbor joining on both single-rate and gamma-corrected distances, and maximum likelihood, were able to recover these relationships for the 12S gene. Parsimony analyses of the 12S data resulted in a relatively strongly supported placement of Peromyscus eremicus that conflicts with that suggested by cyt b and all other data. There is extreme among-site rate variation in the 12S sequences and moderate levels in the cyt b sequences. This highly skewed distribution of rates in the 12S gene makes phylogenetic analyses of these sequences particularly susceptible to the misleading effects of nonindependence and other nonrandom noise, suggesting that phylogenetic analyses of data sets that contain a great deal of among-site rate variation be interpreted with caution.

Animals↗

PubMed2002

Bayesian phylogenetic analysis supports monophyly of ambulacraria and of cyclostomes.

Vertebrates are part of the phylum Chordata, itself part of a three-phylum group known as the deuterostomes. Despite extensive phylogenetic analysis of the deuterostome animals, several unresolved relationships remain. These include the relationship between the three deuterostome phyla (chordates, echinoderms and hemichordates), and the monophyletic or paraphyletic origin of the cyclostomes (hagfish and lampreys). Using robust Bayesian statistical analysis of 18S ribosomal DNA, mitochondrial genes and nuclear protein-coding DNA, we find strong support for a hemichordate-echinoderm clade, and for monophyly of the cyclostomes.

Animals↗

PubMed2005

Phylogenetic analysis of the gag region encoding the matrix protein of small ruminant lentiviruses: comparative analysis and molecular epidemiological applications.

Little sequence information exists on the matrix-protein (MA) encoding region of small ruminant lentiviruses (SRLV). Fifty-two novel sequences were established and permitted a first phylogenetic analysis of this region of the SRLV genome. The variability of the MA encoding region is higher compared to the gag region encoding the capsid protein and surprisingly close to that reported for the env gene. In contrast to primate lentiviruses, the deduced amino acid sequences of the N- and C-terminal domains of MA are variable. This permitted to pinpoint a basic domain in the N-terminal domain that is conserved in all lentiviruses and likely to play an important functional role. Additionally, a seven amino acid insertion was detected in all MVV strains, which may be used to differentiate CAEV and MVV isolates. A molecular epidemiology analysis based on these sequences indicates that the Italian lentivirus strains are closely related to each other and to the CAEV-CO strain, a prototypic strain isolated three decades ago in the US. This suggests a common origin of the SRLV circulating in the monitored flocks, possibly related to the introduction of infected goats in a negative population. Finally, this study shows that the MA region is suitable for phylogenetic studies and may be applied to monitor SRLV eradication programs.

Amino Acid Sequence↗

PubMed2006

Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis.

Mycobacterium tuberculosis strains contain different genomic insertions or deletions called large sequence polymorphisms (LSPs). Distinguishing between LSPs that occur one time versus ones that occur repeatedly in a genomic region may provide insights into the biological roles of LSPs and identify useful phylogenetic markers. We analyzed 163 clinical M. tuberculosis isolates for 17 LSPs identified in a genomic comparison of M. tuberculosis strains H37Rv and CDC1551. LSPs were mapped onto a single-nucleotide polymorphism (SNP)-based phylogenetic tree created using nine novel SNP markers that were found to reproduce a 212-SNP-based phylogeny. Four LSPs (group A) mapped to a single SNP tree segment. Two LSPs (group B) and 11 LSPs (group C) were inferred to have arisen independently in the same genomic region either two or more than two times, respectively. None of the group A LSPs but one group B LSP and five group C LSPs were flanked by IS6110 sequences in the references strains. Genes encoding members of the proline-glutamic acid or proline-proline-glutamic acid protein families were present only in group B or C LSPs. SNP- versus LSP-based phylogenies were also compared. We classified each isolate into 58 LSP types by using a separate LSP-based phylogenetic analysis and mapped the LSP types onto the SNP tree. LSPs often assigned isolates to the correct phylogenetic lineage; however, significant mistakes occurred for 6/58 (10%) of the LSP types. In conclusion, most LSPs occur in genomic regions that are prone to repeated insertion/deletion events and were responsible for an unexpectedly high degree of genomic variation in clinical M. tuberculosis. Group B and C LSPs may represent polymorphisms that occur due to selective pressure and affect the phenotype of the organism, while group A LSPs are preferable phylogenetic markers.

Gene Deletion↗

PubMed2004

Phylogenetic analysis and reclassification of caprine and ovine lentiviruses based on 104 new isolates: evidence for regular sheep-to-goat transmission and worldwide propagation through livestock trade.

We performed a phylogenetic analysis of caprine and ovine lentiviruses using long sequences in gag and pol of 104 new Swiss isolates and six available corresponding database sequences. Forty-five isolates, forming five sequence clusters, were unclassifiable by the present classification. Pairwise DNA distance analysis indicated different categories of relatedness, requiring a new classification system. We propose four principal sequence groups, A-D, which differ by 25-37%. Groups A and B are further divided into subtypes which differ by 15-27%. Group D and four of the seven group A subtypes, A3, A4, A5 and A7, are formed by new Swiss isolates. Molecular epidemiology revealed that Swiss B1 strains differed no more from French, Brazilian or US strains than from each other, suggesting virus propagation through international livestock trade. Furthermore, infection of goats by subtypes A3 or A4 was significantly associated with documented contact with sheep, which also harbor these subtypes, thus indicating regularly occurring sheep-to-goat transmission.

Agriculture↗

PubMed1999

Characterization of cDNAs for mouse lysyl hydroxylase 1, 2 and 3, their phylogenetic analysis and tissue-specific expression in the mouse.

We report on the isolation and characterization of cDNA clones for mouse lysyl hydroxylases 1, 2 and 3 (LH1, LH2, LH3). Phylogenetic analysis using nine lysyl hydroxylase sequences from five species indicates that the isoforms are derived from an ancestral gene by two duplication events, isoforms 1 and 2 being more closely related and having resulted from a more recent duplication than isoform 3. Expression of the isoforms is highly regulated in adult mouse tissues. LH1 is strongly expressed in the liver, heart, lung, skeletal muscle and kidney tissue, LH2 expression is high in the heart, lung, kidney, eye, ovary and placenta, whereas LH3 expression is high in the heart, lung, liver and testis tissue.

3' Untranslated Regions↗

PubMed2005

Phylogenetic analysis and real time PCR detection of a presumbably undescribed Peronospora species on sweet basil and sage.

Downy mildew of sweet basil (Ocimum basilicum) has become a serious disease issue for the producers of sweet basil in Switzerland since it was first recorded in 2001. Reported in Africa in Uganda as early as 1933, major outbreaks of this disease in Europe were first noted in Italy in 1999 and in the USA from 1993. Previous reports have named the pathogen as Peronospora lamii. Its preferential hosts belong to the Lamiaceae family including basils (Ocimum spp.), mints (Menta spp.), sages (Salvia spp.) and other aromatics. This study investigated the taxonomic status of the downy mildew pathogen, using both morphological characters and molecular analysis of the ITS region of the rDNA. The inherent variability of conidial dimensions made species differentiation difficult. Sequence homology and phylogenetic analysis of nine collections of the Peronospora on sweet basil showed unique ITS sequences distinct from those of P. lamii and any other sequenced Peronospora species. This paper describes and illustrates the morphology of this presumably undescribed species of Peronospora. Its taxonomic position and relationships with other related species in the same genus are presented and discussed. In addition to this work, PCR primers for real time PCR analysis have been developed for the specific detection of this downy mildew pathogen from infected tissues or seeds. It is shown that these primers can also be used in classic PCR.

Base Sequence↗

PubMed2001

PhyloBLAST: facilitating phylogenetic analysis of BLAST results.

PhyloBLAST is an internet-accessed application based on CGI/Perl programming that compares a users protein sequence to a SwissProt/TREMBL database using BLAST2 and then allows phylogenetic analyses to be performed on selected sequences from the BLAST output. Flexible features such as ability to input your own multiple sequence alignment and use PHYLIP program options provide additional web-based phylogenetic analysis functionality beyond the analysis of a BLAST result.

Internet↗

PubMed1999

Phylogenetic analysis of genus Marinilabilia and related bacteria based on the amino acid sequences of gyrB and emended description of Marinilabilia salmonicolor with Marinilabilia agarovorans as its subjective synonym.

The detailed phylogenetic relationships for genus Marinilabilia and related taxa were analysed by using DNA gyrase B subunit gene (gyrB) sequences. Anaerobic bacteria in the Cytophaga-Flavobacterium-Bacteroides phylum, namely genera Marinilabilia, Bacteroides, Rikenella, Prevotella and Porphyromonas and Cytophaga fermentans, were clustered in the same branch and the facultative anaerobes Marinilabilia and Cytophaga fermentans formed a subcluster in the branch of the anaerobic bacteria. Phylogenetic analysis using 16S rDNA sequences gave a similar result but with a lower bootstrap value for each cluster. The gyrB sequences of Marinilabilia salmonicolor and Marinilabilia agarovorans were the same, and the relatedness of their chromosomal DNA, as determined by DNA-DNA hybridization, was greater than 70%. These genetic aspects led to the conclusion that M. salmonicolor IFO 15948T and M. agarovorans IFO 14957T belong to a single species. Since M. salmonicolor was described first, as Cytophaga salmonicolor, M. salmonicolor is a senior subjective synonym of M. agarovorans. Therefore, the name M. salmonicolor should be retained and strain IFO 14957T should be reclassified as M. salmonicolor. However, the agar-degrading ability of strain IFO 14957T is a prominent biochemical characteristic. It is therefore proposed that strain IFO 14957T should be renamed M. salmonicolor biovar agarovorans.

Amino Acid Sequence↗