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.
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Douglas S. Stones •
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.
"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.
The rDNA is the transcribed DNA, giving a rRNA.
I have been asked by my supervisor to look for 18S rRNA so that I can create the phylogenetic tree for pig. But I am a little bit confiuse on how to work on it.
That is not an answer to the question. If you want to ask a new question, please go ahead, but be a bit more precise about your 'confusion' and how you look at it.
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Thanks for taking the trouble answering this question.