What'S The Difference Between 18S Rrna And 18S Rdna?

Question

[Douglas S. Stones]

The 18S rRNA is frequently used in phylogeny (see http://en.wikipedia.org/wiki/18S_ribosomal_RNA). For example, GenBank ref. AY742884 (which I accessed from here) includes

LOCUS       AY742884                1846 bp    DNA     linear   INV 17-OCT-2005
DEFINITION  Physopelta gutta 18S ribosomal RNA gene, partial sequence.

which makes me confused, since it uses both terms DNA and RNA.

I'm after a straightforward explanation of the difference between 18S rRNA and 18S rDNA.

[Douglas S. Stones]

Thanks for taking the trouble answering this question.

Answer 1

[Dave Lunt]

Although you sometimes see people getting muddled in Methods sections, nobody sequences rRNA in phylogenetic studies these days. They PCR from a DNA (not RNA) template and sequence that- it is DNA from start to finish. Not so at the start of the molecular phylogenetics era when rRNA sequences actually came directly from RNA extracted from cells. Giovanni is spot on though, and rRNA should be treated as a name for the product of the gene we are talking about, e.g. "I sequenced single stranded binding protein" usually doesn't mean you did anything with a protein, rather sequenced the gene and predicted the amino acids.

Answer 2

[Giovanni M Dall'Olio]

"18S ribosomal RNA" is the name of the product of the gene. You should take it as a name, as if it were the name of a protein. The AY742884 entry identifies the DNA sequence that encodes for the 18S rRNA.

Answer 3

[Pierre Lindenbaum]

The rDNA is the transcribed DNA, giving a rRNA.