Is the {16S-23S} {rRNA} internal transcribed spacer region a good tool for use in molecular systematics and population genetics? A case study in cyanobacteria

  • Boyer S
  • Flechtner V
  • Johansen J
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We amplified, {TA-cloned}, and sequenced the {16S-23S} internal transcribed spacer ({ITS)} regions from single isolates of several cyanobacterial species, Calothrix parietina, Scytonema hyalinum, Coelodesmium wrangelii, Tolypothrix distorta, and a putative new genus (isolates {SRS6} and {SRS70)}, to investigate the potential of this {DNA} sequence for phylogenetic and population genetic studies. All isolates carried {ITS} regions containing the sequences coding for two {tRNA} molecules ({tRNAn} Ile and {tRNA} Ala). We retrieved additional sequences without {tRNA} features from both C. parietina and S. hyalinum. Furthermore, in S. hyalinum, we found two of these non-{tRNA-encoding} regions to be identical in length but different in sequence. This is the first report of {ITS} regions from a single cyanobacterial isolate not only different in configuration, but also, within one configuration, different in sequence. The potential of the {ITS} region as a tool for studying molecular systematics and population genetics is significant, but the presence of multiple nonidentical {rRNA} operons poses problems. Multiple nonidentical {rRNA} operons may impact both studies that depend on comparisons of phylogenetically homologous sequences and those that employ restriction enzyme digests of {PCR} products. We review current knowledge of the numbers and kinds of {16S-23S} {ITS} regions present across bacterial groups and plastids, and we discuss broad patterns congruent with higher-level systematics of prokaryotes.

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  • S.L.a Boyer

  • V.R.a b Flechtner

  • J.R.a Johansen

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