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PubMed2000

GenBank.

The GenBank((R))sequence database incorporates publicly available DNA sequences of >55 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (Web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping and protein structure information, plus the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov

Animals↗
PubMed2002

GenBank.

The GenBank sequence database incorporates publicly available DNA sequences of more than 105 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of World Wide Web retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov.

Animals↗
PubMed1994

Comparative studies of iridoviruses: further support for a new classification.

Changes in the classification of invertebrate iridoviruses (IVs) (Iridoviridae) have recently been proposed (Williams and Cory, 1994). The previous system of naming isolates according to the host and sequence of discovery (IV type 1, IV2, IV3, etc.) is not adequate for the purposes of taxonomy, since iridovirus isolates may infect many species, including hosts from diverse invertebrate orders. The new system of invertebrate iridovirus nomenclature, as with several other virus families, is based on geographical origin. Proposals have been made, based on DNA hybridization and other characteristics, by which invertebrate iridovirus isolates can be assigned to one of four recognized complexes, or considered as candidates for alternative assignations. This study reports comparative data on the DNA of 14 invertebrate iridovirus isolates used in the Williams and Cory study plus the two type vertebrate iridoviruses, frog virus 3 and flounder lymphocystis disease virus. DNA studies support the validity of assigning several isolates a common name and of grouping the known isolates into four complexes. The detection of such complexes is in broad agreement with previous serological studies. A previously undescribed isolate (San Miguel IV) obtained from the lepidopteran pest Anticarsia gemmatalis (Lep.: Noctuidae) has been initially characterized following the procedures recommended by Williams and Cory. DNA hybridization and Southern blot analysis identified this isolate as a new member of the Polyiridovirus complex. The San Miguel IV MSP gene was identified and a central fragment of ca. 719 bp was recovered by PCR amplification. The restriction endonuclease profiles (5 enzymes) of this isolate were distinct from others previously described.

Animals↗
PubMed2003

GenBank.

GenBank (R) is a comprehensive sequence database that contains publicly available DNA sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Animals↗
PubMed2004

GenBank: update.

GenBank is a comprehensive database that contains publicly available DNA sequences for more than 140 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin program and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Animals↗
PubMed2005

GenBank.

GenBank is a comprehensive database that contains publicly available DNA sequences for more than 165,000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps to ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

Animals↗
PubMed1996

Phenotype variability of identical genotypes: the need for a combined approach in cyanobacterial taxonomy demonstrated on Merismopedia-like isolates

Five Merismopedia-like cyanobacterial strains were collected from microbial mats at Norderney Island, subcultured in the laboratory, and finally grown as unicyanobacterial cultures. As a sixth strain, Merismopedia glauca from the rising dbl quote, left (low)Sammlung von Algenkulturen" at Gottingen (SAG) was used for comparisons. According to morphological and physiological characteristics initially observed in the field and during initial subculturing, the five strains were assigned to the species Merismopedia glauca, Merismopedia punctata, or Merismopedia elegans. However, after prolonged maintenance under laboratory conditions, the formation of platelet-like colonies stopped, whereas cell sizes, production of extracellular polymeric substances, and division patterns were stably maintained. These physiological and morphological parameters allowed us to divide the six strains into two clusters. This division was further supported by the profiling of total cell protein and phycobilisomes using SDS-PAGE. The nearly complete 16S rDNA sequence of three of the six isolates was determined. The comparative sequencing analysis revealed an almost 100% identity of these three Merismopedia-like strains. The evolutionary distance dendrogram constructed placed this Merismopedia cluster into a common line of descent with Synechocystis sp. strain PCC6906. Based on the analysis of common stretches of 1,050 nucleotides, the overall similarity between the sequence types of rising dbl quote, left (low)Merismopedia" and rising dbl quote, left (low)Synechocystis" is 96-97%. The values of the different methods for taxonomic classification of unicyanobacterial strains, the relationship of the cyanobacterial genera Merismopedia, Synechococcus, Synechocystis, and Eucapsis sp., and the functional role of different Merismopedia morphologies within microbial mats are discussed. It is suggested that all analyzed Merismopedia strains be combined into one species, namely Merismopedia punctata Meyen (1839).

Journal Article↗
PubMed1999

Taxonomy and phylogenetic relationships of early Miocene catarrhines from Sihong, China.

Paleontological investigations at sites in Sihong County, Jiangsu Province, China since 1981 have yielded a sizeable collection of previously undescribed fossil catarrhines from the Xiacaowan Formation. The associated vertebrate fauna indicates a late early Miocene age (correlating with MN 4, late Orleanian of Europe, approximately 17-18 Ma), which establishes the Sihong primates as the earliest known catarrhines from Eurasia. The fossil primates are assigned to two species: Dionysopithecus shuangouensis Li, 1978 and Platodontopithecus jianghuaiensis Gu & Lin, 1983. Although the new material from Sihong consists mainly of isolated teeth, it does provide important new information on the anatomy of Dionysopithecus and Platodontopithecus that helps to clarify their phylogenetic and taxonomic status. Previous studies have suggested that the Sihong catarrhines might be closely related to the proconsulids from the early Miocene of East Africa. However, with more extensive material available for comparison, the Sihong primates can now be shown to share a number of key derived features with pliopithecids. This new evidence helps to resolve a longstanding problem concerning the origins of the Pliopithecidae. It was previously considered that specialized pliopithecids migrated into Europe during MN 5, originating from an unknown antecedent and location in Africa. Recognition that the Sihong primates have affinities with pliopithecids, but are more primitive, suggests that the initial differentiation and diversification of the clade may have taken place in Asia rather than Africa. The earliest Eurasian catarrhines probably migrated into tropical Asia as part of a major faunal interchange with Africa that occurred during MN 3.

Animals↗
PubMed2006

Genetic characterization of tick-borne flaviviruses: new insights into evolution, pathogenetic determinants and taxonomy.

Here, we analyze the complete coding sequences of all recognized tick-borne flavivirus species, including Gadgets Gully, Royal Farm and Karshi virus, seabird-associated flaviviruses, Kadam virus and previously uncharacterized isolates of Kyasanur Forest disease virus and Omsk hemorrhagic fever virus. Significant taxonomic improvements are proposed, e.g. the identification of three major groups (mammalian, seabird and Kadam tick-borne flavivirus groups), the creation of a new species (Karshi virus) and the assignment of Tick-borne encephalitis and Louping ill viruses to a unique species (Tick-borne encephalitis virus) including four viral types (i.e. Western Tick-borne encephalitis virus, Eastern Tick-borne encephalitis virus, Turkish sheep Tick-borne encephalitis virus and Louping ill Tick-borne encephalitis virus). The analyses also suggest a complex relationship between viruses infecting birds and those infecting mammals. Ticks that feed on both categories of vertebrates may constitute the evolutionary bridge between the three distinct identified lineages.

Animals↗
PubMedDate not supplied

Biosystematics and diversity amongst novel carboxydotrophic actinomycetes.

Fifty-four carboxydotrophic actinomycetes isolated from soils and composts were compared through 119 unit characters with representative mesophilic and thermophilic streptomycetes. The data were examined using the Jaccard, pattern and simple matching coefficients and clustering achieved using the unweighted pair group method with arithmetic averages algorithm. Acceptable cophenetic correlation and test error values allowed confidence to be placed in the resultant numerical taxonomies. The carboxydotrophic actinomycetes, which were distinct from cluster-groups corresponding to the mesophilic and thermophilic streptomycetes, formed two major cluster-groups the members of which were examined for the presence of diagnostic chemical markers. All but two of the carboxydotrophic actinomycetes had a profile of chemical properties consistent with their assignment to the genus Streptomyces. Quantitative fatty acid data were examined using the SIMCA package and the two statistically significant groups obtained corresponded with the cluster-groups circumscribed in the numerical phenetic analysis. Members of the two groups were also distinguished on the basis of their phospholipid composition. The two strains that contained meso-as opposed to LL-diaminopimelic acid in their peptidoglycan also showed a distinct chemotaxonomic profile. It was concluded that the carboxydotrophic actinomycetes form a novel and taxonomically diverse group.

Actinomycetales↗
PubMed1984

DNA homology studies in the taxonomy of dermatophytes.

The taxonomy of the dermatophyte genera Trichophyton, Microsporum and Epidermophyton was investigated by determinations of DNA homology. DNA extracted from 10 isolates (seven species) of dermatophytes was reannealed by hydroxyapatite chromatography. DNA homology levels of 65-80% corresponded to species within a single genus. There was a general agreement with established classification, particularly in assigning species to separate genera. DNA from the Trichophyton state of Arthroderma benhamiae (NCPF 456) showed 71 and 76% homology with DNA from T. mentagrophytes (NCPF 224) and T. rubrum (NCPF 5034) respectively. T. terrestre showed low homology (25%) when compared with the other species of dermatophytes tested.

Arthrodermataceae↗
PubMed2006

Specific classification of elibrary resources says more about users' preferences.

BACKGROUND: Medical Subject Headings (MeSH) are a hierarchical taxonomy of over 42,000 descriptors designed to classify scientific literature; it is hierarchical with generic high order headings and specific low order headings. Over 1,000 resources in the Primary Care Electronic Library (PCEL - www.pcel.info) were classified with MeSH. METHODS: Each of the entries or resources in the primary care digital library was assigned up to five MeSH terms. We compared whether the most generic or specific MeSH term ascribed to each resource best predicted user preferences. RESULTS: over the four month period analysed statistically significant differences were found for resources according to specific key MeSH terms they were classified by. This result was not repeated for generic key MeSH terms. CONCLUSIONS: Analysis of the use of specific MeSH terms reveals user preferences that would have otherwise remained obscured. These preferences are not found if more generic MeSH terms are analysed.

Consumer Behavior↗
PubMedDate not supplied

[A proposal for Salmonella nomenclature].

A single species, composed of six subspecies, was found in the genus Salmonella following a numerical taxonomy and a study of the DNA relatedness (see p. 223, Le Minor et al.). The Salmonella nomenclature is herein updated to take into account modern taxonomic knowledge. The single Salmonella species is S. choleraesuis (type species). Six subspecies are proposed: (1) S. choleraesuis subsp. choleraesuis subsp. nov. is composed of all Salmonella strains formerly assigned to the subgenus I; (2) S. choleraesuis subsp. salamae subsp. nov. corresponds to the former subgenus II; (3) S. choleraesuis subsp. arizonae comb. nov. is composed of monophasic serovars of the former subgenus III ("Arizona"); (4) S. choleraesuis subsp. diarizonae subsp. nov. is composed of diphasic serovars of the former subgenus III ("Arizona"); (5) S. choleraesuis subsp. houtenae subsp. nov. corresponds to the former subgenus IV; and (6) S. choleraesuis subsp. bongori subsp. nov. is composed of strains positive for dulcitol fermentation, ONPG, and KCN tests. Type strains are proposed for each subspecies. The name of S. choleraesuis subsp. choleraesuis serotypes (e.g. typhimurium) should be used without italicization or underlining (e.g. S. choleraeusis subsp. choleraesuis ser. typhimurium). A practical and unofficial use of non-italicized serotype names is discussed.

Salmonella↗
PubMed2001

Numerical taxonomy of microorganisms isolated from goat cheese made in Chile.

118 strains of heterotrophic microorganisms were isolated from goat cheese produced domestically in the IV Region of Northern Chile (Serene, Ovalle, and Illapel) and sold in supermarkets in Valparaíso, Chile. The results of 89 phenotypic tests were numerically analyzed against 17 reference strains, using the simple matching coefficient (S(SM)). Thirteen phena were found at a 78% similarity level. Five of them (A, B, C, D, and E) were assigned to the family Enterobacteriaceae, phenon F was identified as belonging to the genus Aeromonas and strains of phenon G were assigned to the genus Acinetobacter. The other phena were identified as being members of the genera Bacillus (H, I, and J), Staphylococcus (K), Enterococcus (L), and Micrococcus (M). Approximately 19% of the isolates were Escherichia coli and 27%, Staphylococcus aureus.

Animals↗
PubMed2002

Molecular characterisation of Babesia canis canis and Babesia canis vogeli from naturally infected European dogs.

The morphologically small Babesia species isolated from naturally infected dogs in Europe, Japan, and US are described as Babesia gibsoni despite the fact that molecular techniques show that they should be assigned to two or three separate taxons. The morphologically large Babesia isolated from dogs in Europe, Africa, and US were generally classified as B. canis until it was proposed to distinguish three related, albeit genetically distinct subspecies of this genus, namely B. canis canis, B. canis rossi, and B. canis vogeli. The insight into the molecular taxonomy of canine piroplasms is, however, limited because only partial small subunit ribosomal RNA (ssrRNA) sequence data exist for two species from the B. canis group. In this work, we molecularly characterised natural Babesia infections in 11 dogs from Croatia, France, Italy, and Poland. These infections were diagnosed as caused by B. canis canis and B. canis vogeli based on the analysis of the complete sequence of the ssrRNA genes. Phylogenetic analysis confirmed that the large Babesia species of dogs belong the to the Babesia sensu stricto clade, which includes species characterised by transovarial transmission in the tick vectors and by exclusive development inside the mammalian host erythrocytes. The new data facilitate the reliable molecular diagnosis of the subspecies of B. canis.

Animals↗
PubMed2003

Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora.

Genera currently assigned to the Saccharomycetaceae have been defined from phenotype, but this classification does not fully correspond with species groupings determined from phylogenetic analysis of gene sequences. The multigene sequence analysis of Kurtzman and Robnett [FEMS Yeast Res. 3 (2003) 417-432] resolved the family Saccharomycetaceae into 11 well-supported clades. In the present study, the taxonomy of the Saccharomyctaceae is evaluated from the perspective of the multigene sequence analysis, which has resulted in reassignment of some species among currently accepted genera, and the proposal of the following five new genera: Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora.

Kluyveromyces↗
PubMed1995

Molecular phylogeny of annexins and identification of a primitive homologue in Giardia lamblia.

The homologous repeats of annexin tetrads are believed to have originated by successive duplication and fusion from a putative monomeric precursor, but neither the nature of their ancestor nor the events leading to the formation of different subfamilies have been elucidated. We have performed molecular phylogenetic analysis of aligned annexin nucleotide and amino acids sequences to characterize subfamily branching, to delineate the temporal order of appearance of individual repeat units, and to gain insight into the origin and nature of the primordial unit. All extant annexins appear to have a common tetrad precursor that may have originated from a progenitor unit resembling repeat 3, followed by the generation of repeats 4, 1, and 2 from a more evolved progenitor with subsequent fusion. Repeat sequences of the earliest human annexins VII and XIII were used to identify alpha-giardin genes as primitive homologues from the unicellular protozoan Giardia lamblia, which diverged from eukaryote lineage 1-1.5 billion yr ago. The significant homology between alpha-giardins and annexins suggested that the cell membrane adhesive role of these proteins may be a common, fundamental property of the annexin C-terminal core region. Purported annexin VII of Dictyostelium discoideum was reclassified as new annexin XIV, three Caenorhabditis elegans genes were assigned to new subfamilies XV, XVI, and XVII, and plant annexin XVIII from Medicago sativa was among the earliest diverging subfamilies. Annexins I and II were found to be closely related, but analysis of protein mutation rates confirmed that the former is evolving up to three times more rapidly. The inclusion of early phyla in annexin taxonomy provides a useful basis for assessing the structural and functional changes associated with annexin evolution.

Amino Acid Sequence↗
PubMed2004

Can whole genome analysis refine the taxonomy of the genus Rhodococcus?

The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.

Actinobacteria↗