1887

Abstract

In many prokaryotic species, 16S rRNA genes are present in multiple copies, and their sequences in general do not differ significantly owing to concerted evolution. At the time of writing, the genus of the family comprises nine species with validly published names, all of which possess two to four highly heterogeneous 16S rRNA genes. Existence of multiple heterogeneous 16S rRNA genes makes it difficult to reconstruct a biological phylogenetic tree using their sequence data. If the orthologous gene is able to be discriminated from paralogous genes, a tree reconstructed from orthologous genes will reflect a simple biological phylogenetic relationship. At present, however, we have no means to distinguish the orthologous rRNA operon from paralogous ones in the members of the family . In this study, we found that the dihydroorotate oxidase gene, , was present in the immediate upstream of one 16S rRNA gene in each of ten strains of the family whose genome sequences have been determined, and the direction of the gene was opposite to that of the 16S rRNA genes. In two other strains whose genome sequences have been determined, the gene was present in far separated positions. We designed PCR primer sets to amplify DNA fragments encompassing a region from the conserved region of the gene to a conserved region of the tRNA-Ala gene or the 23S rRNA gene to determine the 16S rRNA gene sequences preceded by the gene, and to see if the gene is conserved in the immediate upstream of rRNA operon(s) in the type strains of the type species of 28 genera of the family . Seventeen type strains, including the ten strains mentioned above, gave amplified DNA fragments of approximately 4000 bp, while eleven type strains, including the two strains mentioned above, did not give any PCR products. These eleven strains are members of the Clade I haloarchaea, originally defined by Walsh (2004) and expanded by Minegishi (2010). Analysis of contig sequences of three strains belonging to the Clade I haloarchaea also revealed the absence of the gene in the immediate upstream of any 16S rRNA genes. It may be scientifically sound to hypothesize that during the evolution of members of the family , a gene transposition event happened in one group and this was followed by subsequent speciation processes in each group, yielding species/genera of the Clade I group and ‘the rest’ of the present family .

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2012-01-01
2024-03-19
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