I work with nematode (eukaryote) ribosomal DNA, In the literature I see that some times the 28S gene is refered to as the 26S gene or vice versa for different nematode species. Can anybody tell me whats the difference ?

I don't know for definite, but I would just assume that the genes are different sizes depending on the species. It's the same gene, but I assume the genes/gene products are slightly different sizes.

 

The "S" refers to the Svedburg unit of molecular size, referring to the weight at which molecules sediment in centrifuges.

Both refer to the same gene. Initially the large subunit of nematodes was determined to be 26S, however comparisons with other organisms indicated that it should be 28s. Due to historic reasons both names stuck (as it is both a name as well as a classifier). Generally you will find older publications with 26s, newer papers that do not only deal with nematodes often call it 28s rRNA, and some compromise with 26/28s. "Real" 26s rRNA is generally found in plants, yeast and protozoa.

Thanks very much to both of you guys, very informative and helpful.