The Experts below are selected from a list of 276 Experts worldwide ranked by ideXlab platform
Yves Van De Peer - One of the best experts on this subject based on the ideXlab platform.
-
Database on the structure of Small Ribosomal Subunit RNA.
Nucleic acids research, 1997Co-Authors: Yves Van De Peer, P De Rijk, J Jansen, R. De WachterAbstract:The Antwerp database on Small Ribosomal Subunit RNA now offers more than 6000 nucleotide sequences (August 1996). All these sequences are stored in the form of an alignment based on the adopted secondary structure model, which is corroborated by the observation of compensating substitutions in the alignment. Besides the primary and secondary structure information, literature references, accession numbers and detailed taxonomic information are also compiled. For ease of use, the complete database is made available to the scientific community via World Wide Web at URL http://rrna.uia.ac.be/ssu/ .
-
the evolution of stramenopiles and alveolates as derived by substitution rate calibration of Small Ribosomal Subunit rna
Journal of Molecular Evolution, 1996Co-Authors: Yves Van De Peer, Gert Van Der Auwera, R. De WachterAbstract:The substitution rate of the individual positions in an alignment of 750 eukaryotic Small Ribosomal Subunit RNA sequences was estimated. From the resulting rate distribution, an equation was derived that gives a more precise relationship between sequence dissimilarity and evolutionary distance than hitherto available. Trees constructed on the basis of evolutionary distances computed by this new equation for Small Ribosomal Subunit RNA sequences from ciliates, apicomplexans, dinoflagellates, oomycetes, hyphochytriomycetes, bicosoecids, labyrinthuloids, and heterokont algae show a more consistent tree topology than trees constructed in the absence of “substitution rate calibration.” In particular, they do not suffer from anomalies caused by the presence of extremely long branches.
-
Database on the structure of Small Ribosomal Subunit RNA.
Nucleic acids research, 1996Co-Authors: Yves Van De Peer, P De Rijk, S Nicolaï, R. De WachterAbstract:The Antwerp database on Small Ribosomal Subunit RNA offers over 4300 nucleotide sequences (August 1995). All these sequences are stored in the form of an alignment based on the adopted secondary structure model, which in turn is corroborated by the observation of compensating substitutions in the alignment. Besides the primary and secondary structure information, literature references, accession numbers and detailed taxonomic information are also compiled. The complete database is made available to the scientific community through anonymous ftp and World Wide Web(WWW).
-
Investigation of fungal phylogeny on the basis of Small Ribosomal Subunit RNA sequences
Molecular Microbial Ecology Manual, 1995Co-Authors: Yves Van De Peer, Rupert De WachterAbstract:A study published in 1989 [15] on the evolutionary position of fungi within the eukaryotic realm as derived from the structure of Small Ribosomal Subunit RNA comprised only 4 fungal SSU rRNA sequences (SSU rRNA is Small Ribosomal Subunit RNA, i.e. the 16S rRNA of prokaryotes, the 18S rRNA of eukaryotes). At present, December 1993, more than 110 complete or nearly complete SSU rRNA sequences from fungi have been published. This increase can be ascribed to the fact that SSU rRNA has proven an excellent molecule for the reconstruction of phylogeny of bacterial as well as eukaryotic lineages, for reasons enumerated by Woese [41] and Sogin [30].
-
Database on the structure of Small Ribosomal Subunit RNA.
Nucleic acids research, 1994Co-Authors: Yves Van De Peer, P De Rijk, I Van Den Broeck, R. De WachterAbstract:The database on Small Ribosomal Subunit RNA structure contains (June 1994) 2824 nucleotide sequences. All these sequences are stored in the form of an alignment based on the adopted secondary structure model, which in turn is corroborated by the observation of compensating substitutions in the alignment. The complete database is made available to the scientific community through anonymous ftp on our server in Antwerp. A special effort was made to improve electronic retrieval and a program is supplied that allows to create different file formats. The database can also be obtained from the EMBL nucleotide sequence library.
R. De Wachter - One of the best experts on this subject based on the ideXlab platform.
-
Database on the structure of Small Ribosomal Subunit RNA.
Nucleic acids research, 1997Co-Authors: Yves Van De Peer, P De Rijk, J Jansen, R. De WachterAbstract:The Antwerp database on Small Ribosomal Subunit RNA now offers more than 6000 nucleotide sequences (August 1996). All these sequences are stored in the form of an alignment based on the adopted secondary structure model, which is corroborated by the observation of compensating substitutions in the alignment. Besides the primary and secondary structure information, literature references, accession numbers and detailed taxonomic information are also compiled. For ease of use, the complete database is made available to the scientific community via World Wide Web at URL http://rrna.uia.ac.be/ssu/ .
-
the evolution of stramenopiles and alveolates as derived by substitution rate calibration of Small Ribosomal Subunit rna
Journal of Molecular Evolution, 1996Co-Authors: Yves Van De Peer, Gert Van Der Auwera, R. De WachterAbstract:The substitution rate of the individual positions in an alignment of 750 eukaryotic Small Ribosomal Subunit RNA sequences was estimated. From the resulting rate distribution, an equation was derived that gives a more precise relationship between sequence dissimilarity and evolutionary distance than hitherto available. Trees constructed on the basis of evolutionary distances computed by this new equation for Small Ribosomal Subunit RNA sequences from ciliates, apicomplexans, dinoflagellates, oomycetes, hyphochytriomycetes, bicosoecids, labyrinthuloids, and heterokont algae show a more consistent tree topology than trees constructed in the absence of “substitution rate calibration.” In particular, they do not suffer from anomalies caused by the presence of extremely long branches.
-
Database on the structure of Small Ribosomal Subunit RNA.
Nucleic acids research, 1996Co-Authors: Yves Van De Peer, P De Rijk, S Nicolaï, R. De WachterAbstract:The Antwerp database on Small Ribosomal Subunit RNA offers over 4300 nucleotide sequences (August 1995). All these sequences are stored in the form of an alignment based on the adopted secondary structure model, which in turn is corroborated by the observation of compensating substitutions in the alignment. Besides the primary and secondary structure information, literature references, accession numbers and detailed taxonomic information are also compiled. The complete database is made available to the scientific community through anonymous ftp and World Wide Web(WWW).
-
Database on the structure of Small Ribosomal Subunit RNA.
Nucleic acids research, 1994Co-Authors: Yves Van De Peer, P De Rijk, I Van Den Broeck, R. De WachterAbstract:The database on Small Ribosomal Subunit RNA structure contains (June 1994) 2824 nucleotide sequences. All these sequences are stored in the form of an alignment based on the adopted secondary structure model, which in turn is corroborated by the observation of compensating substitutions in the alignment. The complete database is made available to the scientific community through anonymous ftp on our server in Antwerp. A special effort was made to improve electronic retrieval and a program is supplied that allows to create different file formats. The database can also be obtained from the EMBL nucleotide sequence library.
-
Ribosomal RNA as a tool for studying evolution
Belgian Journal of Botany, 1992Co-Authors: Yves Van De Peer, Anne Goris, Jean-marc Neefs, P De Rijk, Lydia Hendriks, R De Baere, R. De WachterAbstract:Large databases containing hundreds of sequences are available for 5S Ribosomal RNA, Small Ribosomal Subunit RNA and large Ribosomal Subunit RNA. At the moment, Small Ribosomal Subunit RNA is probably the most appropriate molecule for phylogenetic analysis, due to the large number of available sequences covering a wide range of different organisms, its large chain length and low evolutionary rate. Using this molecule, evolutionary relationships ranging from kingdom level to genus level can be studied. Different natural groups can be distinguished within the three domains Bacteria, Archaea and Eucarya. Comparison of evolutionary trees, constructed by means of Small Ribosomal Subunit rRNA and the far Smaller 5S rRNA for several eukaryotic groups of organisms, show congruencies as well as discrepancies. Although the same clusters can be distinguished, the observed branching order between these groups is different.
Rupert De Wachter - One of the best experts on this subject based on the ideXlab platform.
-
Investigation of fungal phylogeny on the basis of Small Ribosomal Subunit RNA sequences
Molecular Microbial Ecology Manual, 1995Co-Authors: Yves Van De Peer, Rupert De WachterAbstract:A study published in 1989 [15] on the evolutionary position of fungi within the eukaryotic realm as derived from the structure of Small Ribosomal Subunit RNA comprised only 4 fungal SSU rRNA sequences (SSU rRNA is Small Ribosomal Subunit RNA, i.e. the 16S rRNA of prokaryotes, the 18S rRNA of eukaryotes). At present, December 1993, more than 110 complete or nearly complete SSU rRNA sequences from fungi have been published. This increase can be ascribed to the fact that SSU rRNA has proven an excellent molecule for the reconstruction of phylogeny of bacterial as well as eukaryotic lineages, for reasons enumerated by Woese [41] and Sogin [30].
-
Evolutionary Relationships Among Higher Fungi Inferred From Small Ribosomal-Subunit Rna Sequence-analysis
Systematic and Applied Microbiology, 1993Co-Authors: Annick Wilmotte, Yves Van De Peer, Anne Goris, Sabine Chapelle, Raymond De Baere, Bart Nelissen, Jean-marc Neefs, Gregoire L. Hennebert, Rupert De WachterAbstract:The primary structure of the Small Ribosomal Subunit RNA. (SSU rRNA) was determined for 13 species belonging to 10 ascomycete families and for the basidiomycetous anamorphic yeast Rhodotorula glutinis. The sequences were fitted into an alignment of all hitherto published complete or nearly complete eukaryotic Small Subunit rRNA sequences. The evolutionary relationships within the fungi were examined by construction of a tree from 87 SSU rRNA sequences, corresponding to 71 different species, by means of a distance matrix method and bootstrap analysis. It confirms the early divergence of the zygomycetes and the classical division of the higher fungi into basidiomycetes and ascomycetes. The basidiomycetes are divided into true basidiomycetes and ustomycetes. Within the ascomycetes, the major subdivisions hemiascomycetes and euascomycetes can be recognized. However, Schizosaccharomyces pombe does not belong to the cluster of the hemiascomycetes, to which it is assigned in classical taxonomic schemes, but forms a distinct lineage. Among the euascomycetes, the plectomycetes and the pyrenomycetes can be distinguished. Within the hemiascomycetes, the polyphyly of genera like Pichia or Candida and of families like the Dipodascaceae and the Saccharomycetaceae can be observed.
-
Reconstructing evolution from eukaryotic Small-Ribosomal-Subunit RNA sequences: calibration of the molecular clock.
Journal of molecular evolution, 1993Co-Authors: Yves Van De Peer, Jean-marc Neefs, Peter De Rijk, Rupert De WachterAbstract:The detailed descriptions now available for the secondary structure of Small-Ribosomal-Subunit RNA, including areas of highly variable primary structure, facilitate the alignment of nucleotide sequences. However, for optimal exploitation of the information contained in the alignment, a method must be available that takes into account the local sequence variability in the computation of evolutionary distance. A quantitative definition for the variability of an alignment position is proposed in this study. It is a parameter in an equation which expresses the probability that the alignment position contains a different nucleotide in two sequences, as a function of the distance separating these sequences, i.e., the number of substitutions per nucleotide that occurred during their divergence. This parameter can be estimated from the distance matrix resulting from the conversion of pairwise sequence dissimilarities into pairwise distances. Alignment positions can then be subdivided into a number of sets of matching variability, and the average variability of each set can be derived. Next, the conversion of dissimilarity into distance can be recalculated for each set of alignment positions separately, using a modified version of the equation that corrects for multiple substitutions and changing for each set the parameter that reflects its average variability. The distances computed for each set are finally averaged, giving a more precise distance estimation. Trees constructed by the algorithm based on variability calibration have a topology markedly different from that of trees constructed from the same alignments in the absence of calibration. This is illustrated by means of trees constructed from Small-Ribosomal-Subunit RNA sequences of Metazoa. A reconstruction of vertebrate evolution based on calibrated alignments matches the consensus view of paleontologists, contrary to trees based on uncalibrated alignments. In trees derived from sequences covering several metazoan phyla, artefacts in topology that are probably due to a high clock rate in certain lineages are avoided.
-
Evolution of eukaryotes as deduced from Small Ribosomal Subunit RNA sequences
Biochemical Systematics and Ecology, 1993Co-Authors: Yves Van De Peer, Jean-marc Neefs, Peter De Rijk, Rupert De WachterAbstract:Abstract Evolutionary tress based on Small Ribosomal Subunit RNA sequences yield a new perspective on eukaryote evolution. In agreement with classical views regarding evolution, animals, green plants, and fungi form monophyletic groups which seem to have originated nearly simultaneously. The evolution of these organisms took place in a relatively short time interval and is characterized by a massive diversification of life forms. In contrast, the dissimilarity among protoctist Small Ribosomal Subunit RNA sequences is huge and exceeds the diversity seen in the entire prokaryotic world. Furthermore, some Protoctista branch off very soon in eukaryote evolution, while others diverge much later. Based on these Ribosomal RNA data, Protoctista should be regarded as a collection of independent evolutionary lineages. Because the evolutionary distance between the different groups of Protoctista is, in several cases, larger than the evolutionary distance between plants, fungi and animals, the classification of eukaryotes into four kingdoms seems to be artificial and may not reflect true evolutionary relationships. Generally, eukaryotes are considered to be a relatively recently diverged lineage. Based on Ribosomal RNA, however, they seem to be as old as the prokaryote lineages one distinguishes nowadays, namely eubacteria and archaebacteria.
-
Structure of the Small Ribosomal Subunit RNA of the pulmonate snail, Limicolaria kambeul, and phylogenetic analysis of the Metazoa.
FEBS letters, 1992Co-Authors: Birgitta Winnepennickx, Yves Van De Peer, Thierry Backeljau, Rupert De WachterAbstract:The complete nucleotide sequence of the Small Ribosomal Subunit RNA of the gastropod, Limicolaria kambeul, was determined and used to infer a secondary structure model. In order to clarify the phylogenetic position of the Mollusca among the Metazoa, an evolutionary tree was constructed by neighbor-joining, starting from an alignment of Small Ribosomal Subunit RNA sequences. The Mollusca appear to be a monophyletic group, related to Arthropoda and Chordata in an unresolved trichotomy.
Jean-marc Neefs - One of the best experts on this subject based on the ideXlab platform.
-
compilation of Small Ribosomal Subunit rna structures
Nucleic Acids Research, 1993Co-Authors: Jean-marc Neefs, Sabine Chapelle, P De Rijk, Yves Van De Pee, Rupe De WachteAbstract:Abstract The database on Small Ribosomal Subunit RNA structure contained 1804 nucleotide sequences on April 23, 1993. This number comprises 365 eukaryotic, 65 archaeal, 1260 bacterial, 30 plastidial, and 84 mitochondrial sequences. These are stored in the form of an alignment in order to facilitate the use of the database as input for comparative studies on higher-order structure and for reconstruction of phylogenetic trees. The elements of the postulated secondary structure for each molecule are indicated by special symbols. The database is available on-line directly from the authors by ftp and can also be obtained from the EMBL nucleotide sequence library by electronic mail, ftp, and on CD ROM disk.
-
Evolutionary Relationships Among Higher Fungi Inferred From Small Ribosomal-Subunit Rna Sequence-analysis
Systematic and Applied Microbiology, 1993Co-Authors: Annick Wilmotte, Yves Van De Peer, Anne Goris, Sabine Chapelle, Raymond De Baere, Bart Nelissen, Jean-marc Neefs, Gregoire L. Hennebert, Rupert De WachterAbstract:The primary structure of the Small Ribosomal Subunit RNA. (SSU rRNA) was determined for 13 species belonging to 10 ascomycete families and for the basidiomycetous anamorphic yeast Rhodotorula glutinis. The sequences were fitted into an alignment of all hitherto published complete or nearly complete eukaryotic Small Subunit rRNA sequences. The evolutionary relationships within the fungi were examined by construction of a tree from 87 SSU rRNA sequences, corresponding to 71 different species, by means of a distance matrix method and bootstrap analysis. It confirms the early divergence of the zygomycetes and the classical division of the higher fungi into basidiomycetes and ascomycetes. The basidiomycetes are divided into true basidiomycetes and ustomycetes. Within the ascomycetes, the major subdivisions hemiascomycetes and euascomycetes can be recognized. However, Schizosaccharomyces pombe does not belong to the cluster of the hemiascomycetes, to which it is assigned in classical taxonomic schemes, but forms a distinct lineage. Among the euascomycetes, the plectomycetes and the pyrenomycetes can be distinguished. Within the hemiascomycetes, the polyphyly of genera like Pichia or Candida and of families like the Dipodascaceae and the Saccharomycetaceae can be observed.
-
Reconstructing evolution from eukaryotic Small-Ribosomal-Subunit RNA sequences: calibration of the molecular clock.
Journal of molecular evolution, 1993Co-Authors: Yves Van De Peer, Jean-marc Neefs, Peter De Rijk, Rupert De WachterAbstract:The detailed descriptions now available for the secondary structure of Small-Ribosomal-Subunit RNA, including areas of highly variable primary structure, facilitate the alignment of nucleotide sequences. However, for optimal exploitation of the information contained in the alignment, a method must be available that takes into account the local sequence variability in the computation of evolutionary distance. A quantitative definition for the variability of an alignment position is proposed in this study. It is a parameter in an equation which expresses the probability that the alignment position contains a different nucleotide in two sequences, as a function of the distance separating these sequences, i.e., the number of substitutions per nucleotide that occurred during their divergence. This parameter can be estimated from the distance matrix resulting from the conversion of pairwise sequence dissimilarities into pairwise distances. Alignment positions can then be subdivided into a number of sets of matching variability, and the average variability of each set can be derived. Next, the conversion of dissimilarity into distance can be recalculated for each set of alignment positions separately, using a modified version of the equation that corrects for multiple substitutions and changing for each set the parameter that reflects its average variability. The distances computed for each set are finally averaged, giving a more precise distance estimation. Trees constructed by the algorithm based on variability calibration have a topology markedly different from that of trees constructed from the same alignments in the absence of calibration. This is illustrated by means of trees constructed from Small-Ribosomal-Subunit RNA sequences of Metazoa. A reconstruction of vertebrate evolution based on calibrated alignments matches the consensus view of paleontologists, contrary to trees based on uncalibrated alignments. In trees derived from sequences covering several metazoan phyla, artefacts in topology that are probably due to a high clock rate in certain lineages are avoided.
-
Evolution of eukaryotes as deduced from Small Ribosomal Subunit RNA sequences
Biochemical Systematics and Ecology, 1993Co-Authors: Yves Van De Peer, Jean-marc Neefs, Peter De Rijk, Rupert De WachterAbstract:Abstract Evolutionary tress based on Small Ribosomal Subunit RNA sequences yield a new perspective on eukaryote evolution. In agreement with classical views regarding evolution, animals, green plants, and fungi form monophyletic groups which seem to have originated nearly simultaneously. The evolution of these organisms took place in a relatively short time interval and is characterized by a massive diversification of life forms. In contrast, the dissimilarity among protoctist Small Ribosomal Subunit RNA sequences is huge and exceeds the diversity seen in the entire prokaryotic world. Furthermore, some Protoctista branch off very soon in eukaryote evolution, while others diverge much later. Based on these Ribosomal RNA data, Protoctista should be regarded as a collection of independent evolutionary lineages. Because the evolutionary distance between the different groups of Protoctista is, in several cases, larger than the evolutionary distance between plants, fungi and animals, the classification of eukaryotes into four kingdoms seems to be artificial and may not reflect true evolutionary relationships. Generally, eukaryotes are considered to be a relatively recently diverged lineage. Based on Ribosomal RNA, however, they seem to be as old as the prokaryote lineages one distinguishes nowadays, namely eubacteria and archaebacteria.
-
The gene coding for Small Ribosomal Subunit RNA in the basidiomycete Ustilago maydis contains a group I intron.
Nucleic acids research, 1992Co-Authors: Rupert De Wachter, Jean-marc Neefs, Anne Goris, Yves Van De PeerAbstract:The nucleotide sequence of the gene coding for Small Ribosomal Subunit RNA in the basidiomycete Ustilago maydis was determined. It revealed the presence of a group I intron with a length of 411 nucleotides. This is the third occurrence of such an intron discovered in a Small Subunit rRNA gene encoded by a eukaryotic nuclear genome. The other two occurrences are in Pneumocystis carinii, a fungus of uncertain taxonomic status, and Ankistrodesmus stipitatus, a green alga. The nucleotides of the conserved core structure of 101 group I intron sequences present in different genes and genome types were aligned and their evolutionary relatedness was examined. This revealed a cluster including all group I introns hitherto found in eukaryotic nuclear genes coding for Small and large Subunit rRNAs. A secondary structure model was designed for the area of the Ustilago maydis Small Ribosomal Subunit RNA precursor where the intron is situated. It shows that the internal guide sequence pairing with the intron boundaries fits between two helices of the Small Subunit rRNA, and that minimal rearrangement of base pairs suffices to achieve the definitive secondary structure of the 18S rRNA upon splicing.
Anne Goris - One of the best experts on this subject based on the ideXlab platform.
-
Evolutionary Relationships Among Higher Fungi Inferred From Small Ribosomal-Subunit Rna Sequence-analysis
Systematic and Applied Microbiology, 1993Co-Authors: Annick Wilmotte, Yves Van De Peer, Anne Goris, Sabine Chapelle, Raymond De Baere, Bart Nelissen, Jean-marc Neefs, Gregoire L. Hennebert, Rupert De WachterAbstract:The primary structure of the Small Ribosomal Subunit RNA. (SSU rRNA) was determined for 13 species belonging to 10 ascomycete families and for the basidiomycetous anamorphic yeast Rhodotorula glutinis. The sequences were fitted into an alignment of all hitherto published complete or nearly complete eukaryotic Small Subunit rRNA sequences. The evolutionary relationships within the fungi were examined by construction of a tree from 87 SSU rRNA sequences, corresponding to 71 different species, by means of a distance matrix method and bootstrap analysis. It confirms the early divergence of the zygomycetes and the classical division of the higher fungi into basidiomycetes and ascomycetes. The basidiomycetes are divided into true basidiomycetes and ustomycetes. Within the ascomycetes, the major subdivisions hemiascomycetes and euascomycetes can be recognized. However, Schizosaccharomyces pombe does not belong to the cluster of the hemiascomycetes, to which it is assigned in classical taxonomic schemes, but forms a distinct lineage. Among the euascomycetes, the plectomycetes and the pyrenomycetes can be distinguished. Within the hemiascomycetes, the polyphyly of genera like Pichia or Candida and of families like the Dipodascaceae and the Saccharomycetaceae can be observed.
-
The gene coding for Small Ribosomal Subunit RNA in the basidiomycete Ustilago maydis contains a group I intron.
Nucleic acids research, 1992Co-Authors: Rupert De Wachter, Jean-marc Neefs, Anne Goris, Yves Van De PeerAbstract:The nucleotide sequence of the gene coding for Small Ribosomal Subunit RNA in the basidiomycete Ustilago maydis was determined. It revealed the presence of a group I intron with a length of 411 nucleotides. This is the third occurrence of such an intron discovered in a Small Subunit rRNA gene encoded by a eukaryotic nuclear genome. The other two occurrences are in Pneumocystis carinii, a fungus of uncertain taxonomic status, and Ankistrodesmus stipitatus, a green alga. The nucleotides of the conserved core structure of 101 group I intron sequences present in different genes and genome types were aligned and their evolutionary relatedness was examined. This revealed a cluster including all group I introns hitherto found in eukaryotic nuclear genes coding for Small and large Subunit rRNAs. A secondary structure model was designed for the area of the Ustilago maydis Small Ribosomal Subunit RNA precursor where the intron is situated. It shows that the internal guide sequence pairing with the intron boundaries fits between two helices of the Small Subunit rRNA, and that minimal rearrangement of base pairs suffices to achieve the definitive secondary structure of the 18S rRNA upon splicing.
-
Phylogenetic Relationships among Ascomycetes and Ascomycete-like Yeasts as Deduced from Small Ribosomal Subunit RNA Sequences
Systematic and Applied Microbiology, 1992Co-Authors: Lydia Hendriks, Yves Van De Peer, Anne Goris, Jean-marc Neefs, Gregoire L. Hennebert, Marc Vancanneyt, Karel Kersters, Jean-francois Berny, Rupert De WachterAbstract:The primary structure of the Small Ribosomal Subunit RNA (srRNA) molecule of the type strains of the ascosporogenous yeasts Debaryomcyes hansenii, Pichia anomala (synonym: Hansenula anomala), Pichia membranaefaciens, Schizosaccharomyces pombe, Zygosaccharomyces rouxii and Dekkera bruxellensis was determined. The srRNA sequences were aligned with previously published sequences from fungi, including those of 5 candida species, and an evolutionary tree was inferred The srRNA results were compared with chemotaxonomic criteria, e.g. the coenzyme Q system. The heterogeneity of the genera Candida and Pichia is clearly reflected by the srRNA analysis.
-
Ribosomal RNA as a tool for studying evolution
Belgian Journal of Botany, 1992Co-Authors: Yves Van De Peer, Anne Goris, Jean-marc Neefs, P De Rijk, Lydia Hendriks, R De Baere, R. De WachterAbstract:Large databases containing hundreds of sequences are available for 5S Ribosomal RNA, Small Ribosomal Subunit RNA and large Ribosomal Subunit RNA. At the moment, Small Ribosomal Subunit RNA is probably the most appropriate molecule for phylogenetic analysis, due to the large number of available sequences covering a wide range of different organisms, its large chain length and low evolutionary rate. Using this molecule, evolutionary relationships ranging from kingdom level to genus level can be studied. Different natural groups can be distinguished within the three domains Bacteria, Archaea and Eucarya. Comparison of evolutionary trees, constructed by means of Small Ribosomal Subunit rRNA and the far Smaller 5S rRNA for several eukaryotic groups of organisms, show congruencies as well as discrepancies. Although the same clusters can be distinguished, the observed branching order between these groups is different.
-
Evolution of Basidiomycetous Yeasts As Deduced From Small Ribosomal-Subunit Rna Sequences
Systematic and Applied Microbiology, 1992Co-Authors: Yves Van De Peer, Anne Goris, Jean-marc Neefs, Gregoire L. Hennebert, Lydia Hendriks, Marc Vancanneyt, Karel Kersters, Jean-francois Berny, Rupert De WachterAbstract:Complete Small Ribosomal Subunit RNA sequences were used to infer the relationship between several basidiomycetous yeasts, and to resolve the evolutionary position of the basidiomycetes among the fungi. The sequences were determined for Rhodosporidium toruloides (anamorph Rhodotorula glutinis), Filobasidiella neoformans (anamorph Cryptococcus neoformans), Trichosporon cutaneum, Bullera alba and Sporobolomyces roseus. The sequence of Leucosporidium scottii (anamorph formerly named Candida scottii) srRNA has already been published previously (Hendriks et al., J. Mol. Evol. 32, 167-177 (1991)). Using a tree construction program based on a distance matrix, a phylogenetic tree was constructed for all hitherto known fungal srRNA sequences, oomycetes and slime moulds not included. It showed the ascomycetes and the basidiomycetes to be sister groups, probably evolved from a zygomycete-like ancestor and diverged from each other about 840 Myr ago. Among the basidiomycetes, two clearly distinct groups can be recognized, one formed by the teliospore forming species (Rhodosporidium toruloides and Leucosporidium scottii), and the asexual yeast Sporobolomyces roseus, and the other formed by the non-teliospore forming species Filobasidiella neoformans and the asexual yeasts Bullera alba and Trichosporon cutaneum.
