minimum 16S rRNA sequence requirement

Graham Clark graham.clark at lshtm.ac.uk
Tue Jan 14 06:25:04 EST 1997


David Skryja (davadav at bitwise.net) wrote:

>Does anyone know what the minimum amount of 16SrRNA (or rDNA) sequence
>needed to make a species designation? I have two scenarios in mind.
>
>1) For example, the 16S rRNA sequence does not match anything in the
>database, and it looks like a new species
>
>... for scenario #1, how much of the total 16S rRNA must be sequenced
>before one can conlude that it is a new species
>
>2) For example, a partial 16S rRNA sequence obtained is a 99% match with 
>an existing sequence in the database, but only a portion of the 16S rRNA 
>has been sequenced.
>
>... for scenario #2, how much must be sequenced (assume that the 
>sequence will contain variable-region 16S rRNA sequence) to say that 
>allow you to make a specific species identification of a bacterium 

Perhaps the 'rules' are different for bacteria but I do not think species
should be described on the basis of rDNA alone. In eukaryotes there are
examples of bona fide biological species (i.e. unable to interbreed) of 
the ciliate Tetrahymena that have identical small subunit ribosomal RNA
sequences. Therefore identical sequence does not mean same species. 
Likewise there are some organisms where significant intraspecific rDNA
sequence variation has been documented. For example, the parasites 
Giardia intestinalis and Trypanosoma cruzi can show variation of a few 
percent in the small subunit rRNA sequence among isolates but all are 
capable of causing the same disease. Therefore different sequence does 
not mean distinct species.

IMHO you need more than just sequence variation to warrant the 
recognition of a new species. But perhaps bacteriologists feel differently.

Graham
____________________
C. Graham Clark, Ph.D.
Department of Medical Parasitology,
London School of Hygiene and Tropical Medicine,
Keppel Street, London WC1E 7HT, England, G.B.
Tel: ++44-171-927-2351
FAX: ++44-171-636-8739
e-mail: g.clark at lshtm.ac.uk



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