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Assessment of a short phylogenetic marker based on comparisons of 3’end 16S rDNA and 5’end 16S-23S ITS nucleotide sequences of the Bacillus cereus group

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Natural Science 2010年第12期2卷 1113-1118页

作者： sabarimatou yakoubou Jean-Charles Cote Agriculture and Agri-Food Canada Research CentreGouin BlvdSt-Jean-sur-RichelieuCanada Departement des Sciences Biologiques Universite du Quebec a MontrealSucc.“Centre-Ville”MontrealCanada

A short phylogenetic marker previously used in the reconstruction of the Order Bacillales and the genus Bacillus was assessed here at a lower taxa level: species in the Bacillus cereus group: B. anthracis, B. cereus, B. thuringiensis and B. weihenstephanensis. This maker is 220 bp in length. It is a combination of 150 bp at the 3’ end of the 16S rDNA and 70 bp at the 5’ end of the 16S-23S ITS sequence. Three additional Bacillus species, B. halodurans, B. licheniformis and B. subtilis, and Clostridium tetani were included for comparison purposes. A total of eight bacterial species and 12 strains were analyzed. A boot- strapped neighbor-joining tree was inferred from comparative analyses of all allelic sequences of the bacterial species and strains under study. Based on its topology, four major Groups were revealed at the 90% nucleotide sequence identities, Group I to IV. Group I contains all al-leles of the Bacillus cereus group. Group II con-tains all alleles of B. halodurans. Group III con-tains all alleles of B. licheniformis and B. subtilis. Group IV contains all alleles of Clostridium tetani. The 220 bp phylogenetic marker used here could resolve different species from different genera. At the genus level, distant species could be dis-tinguished. Very closely-related species, however, were undistinguishable. Species in the B. cereus group, most notably B. cereus, B. anth- racis and B. thuringiensis, could not be distin- guished. After successfully inferring the phylo- genies of the Order Bacillales and the genus Bacillus, we have met the resolving limit of this short phy-logenetic marker: B. cereus, B. anthracis and B. thuringiensis.

关键词： Bacillus cereus 16S RDNA 16S-23S ITS Phylogeny

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Phylogeny of γ-proteobacteria inferred from comparisons of 3’ end 16S rRNA gene and 5’ end 16S-23S ITS nucleotide sequences

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Natural Science 2010年第6期2卷 535-543页

作者： sabarimatou yakoubou Jean-Charles Cote Agriculture and Agri-Food Canada Research Centre Gouin Blvd St-Jean-sur-Richelieu Québec Canada

The phylogeny of γ-proteobacteria was inferred from nucleotide sequence comparisons of a short 232 nucleotide sequence marker. A total of 64 γ-proteobacterial strains from 13 Orders, 22 families, 40 genera and 59 species were analyzed. The short 232 nucleotide sequence marker used here was a combination of a 157 nucleotide sequence at the 3’ end of the 16S rRNA gene and a 75 nucleotide sequence at the 5’ end of the 16S-23S Internal Transcribed Spacer (ITS) sequence. Comparative analyses of the 3’ end of the 16S rRNA gene nucleotide sequence showed that the last 157 bp were conserved among strains from same species and less conserved in more distantly related species. This 157 bp sequence was selected as the first part in the construction of our nucleotide sequence marker. A bootstrapped neighbor-joining tree based on the alignment of this 157 bp was constructed. This 157 bp could distinguish γ-proteobacterial species from different genera from same family. Closely related species could not be distinguished. Next, an alignment of the 16S-23S ITS nucleotide sequences of alleles from same bacterial strain was performed. The first 75 bp at the 5’ end of the 16S-23S ITS was highly conserved at the intra-strain level. It was selected as the second part in the construction of our nucleotide sequence marker. Finally, a bootstrapped neighbor-joining tree based on the alignment of this 232 bp sequence was constructed. Based on the topology of the neighbour-joining tree, four major Groups, Group I to IV, were revealed with several sub-groups and clusters. Our results, based on the 232 bp sequence were, in general, in agreement with the phylogeny of γ-proteobacteria based on the 16S rRNA gene. The use of this 232 bp sequence as a phylogenetic marker presents several advantages over the use of the entire 16S rRNA gene or the generation of extensive phenotypic and genotypic data in phylogenetic analyses. First, this marker is not allele-dependant. Second, this 232 bp marker conta

关键词： γ-Proteobacteria 16S rRNA 16S-23S ITS Phylogeny

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Phylogeny of the Order Bacillales inferred from 3’16S rDNA and 5’16S-23S ITS nucleotide sequences

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Natural Science 2010年第9期2卷 990-997页

作者： sabarimatou yakoubou Dong Xu Jean-Charles Cote Agriculture and Agri-Food Canada Research CentreGouin BlvdSt-Jean-sur-RichelieuCanada Departement des Sciences Biologiques Universite du Quebec a MontrealSucc.“Centre-Ville”MontrealCanada

A short 220 bp sequence was used to study the taxonomic organization of the bacterial Order Bacillales. The nucleotide sequences of the 3’ end of the 16S rDNA and the 16S-23S Internal transcribed spacer (ITS) were determined for 32 Bacillales species and strains. The data for 40 additional Bacillales species and strains were retrieved directly from Genbank. Together, these 72 Bacillales species and strains encompassed eight families and 21 genera. The 220 bp se- quence used here covers a conserved 150 bp sequence located at the 3’ end of the 16S rDNA and a conserved 70 bp sequence located at the 5’ end of the 16S-23S ITS. A neighbor-joining phylogenetic tree was inferred from comparative analyses of all 72 nucleotide sequences. Eight major Groups were revealed. Each Group was sub-divided into sub-groups and branches. In general, the neighbor-joining tree presented here is in agreement with the currently accepted phylogeny of the Order Bacillales based on phenotypic and genotypic data. The use of this 220 bp sequence for phylogenetic analyses presents several advantages over the use of the entire 16S rRNA genes or the generation of extensive phenotypic and genotypic data. This 220 bp sequence contains 150 bp at the 3’ end of the 16S rDNA which allows discrimination among distantly related species and 70 bp at the 5’ end of the 16S-23S ITS which, owing to its higher percentage of nucleotide sequence divergence, adds discriminating power among closely related species from same genus and closely related genera from same family. The method is simple, rapid, suited to large screening programs and easily accessible to most laboratories.

关键词： Bacillales 16S rDNA 16S-23S ITS Phylogeny

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