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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 53, Issue 3

Phylogenetic relationships between species and related genera inferred from comparison of 3′ end 16S rDNA and 5′ end 16S–23S ITS nucleotide sequences Free

Abstract

The nucleotide sequences of the 3′ end of the 16S rDNA and the 16S–23S internal transcribed spacer (ITS) of 40 species were determined. These included 21 , 9 , 6 , 2 , 1 and 1 species. Comparative sequence analysis of a 220 bp region covering a highly conserved 150 bp sequence located at the 3′ end of the 16S rRNA coding region and a conserved 70 bp sequence located at the 5′ end of the 16S–23S ITS of the 40 species and six sequences available in GenBank were used to infer the phylogenetic relationships between all 46 taxa. When a maximal distance ( , where refers to the number of nucleotide substitutions per site) of 0·31 was introduced as a threshold to determine groupings, 10 phylogenetically distinct clusters were revealed. Twenty-six species were separated in seven groups (I, II, III, IV, V, VI and X), but remained ungrouped. All six species under study were in Group VII. The nine species fell into two distinct groups (VIII and IX). Species with values within 0·05 were considered to be very closely related. These were and in Group II; ‘’ and in Group II; , , and in Group VI; and in Group VI; and in Group VII; and in Group VIII; and , , and in Group X. The phylogenetic classification presented here is, in general, in agreement with current classifications based on phenotypic and molecular data. Our findings suggest, however, that in some cases, further divisions or, conversely, further groupings might be warranted. Should current classifications be re-examined in the light of our results, values of 0·31 and 0·05, as exemplified here, may prove useful threshold values for the grouping of into taxa akin to genera and species, respectively. These thresholds may also reveal, in a different way, bacterial species for which further characterization might be warranted for proper classification and/or reassignment.

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Keyword(s): Dmax, maximal distance, where distance D refers to the number of nucleotide substitutions per site and ITS, internal transcribed spacer
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2003-05-01
2024-04-24
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Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3′ end 16S rDNA and 5′ end 16S–23S ITS nucleotide sequences
Int J Syst Evol Microbiol 53, 695 (2003); https://doi.org/10.1099/ijs.0.02346-0
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