RAPDs with Drosophila

[Stephen W. Schaeffer]

On Sun, 15 May 1994 19:21:22 GMT, Tony Long wrote:

>		I am hoping we can draw Steve Schaeffer into this discussion.  I don't
>think there is a great deal of evidence for microsatellites in D.
>melanogaster at the level seen in other organisms.

     In my study of nucleotide diversity in the alcohol dehydrogenase locus 
of Drosophila pseudoobscura, I have observed little insertion and deletion 
variation that had an appreciable frequency.  My laboratory has sequenced 
3.5 kilobases of the region from over 100 strains of flies collected from 
the North American distribution of the species.  There are 359 nucleotide 
sites that are polymorphic in the data set.  I have just begun to examine 
insertion / deletion variation in this region.  I have discovered one large 
insertion, 1100 base pairs, that has a frequency of one percent.  Most 
insertions and deletions in the region, however, are less than 20 bases in 
length and have frequencies less than five percent.  The number of 
sequence length variants is small compared to variable nucleotide sites (I 
have not estimated the exact number sites recently, but my guess is that 
there are no more than 40 to 50 insertion/ deletion polymorphisms, 1/7 
of the diversity in nucleotide sites). Some of the small sequence length 
variants look like microsatellites because they occur in repeated sequences 
such as CA.  I found one site that has a seven base pair sequence (AGTCTCT) 
repeated two to seven times among the 100 strains.  This seems to be the 
exception rather than the rule.

    In summary, in a close relative of D. melanogaster little diversity is 
observed in sequences that might be called microsatellites.  These data 
suggest that microsatellites will be of little utility compared with 
methods that rapidly assess nucleotide sequence diversity such as SSCPs.

Stephen W. Schaeffer
Institute of Molecular Evolutionary Genetics
The Pennsylvania State University