An inefficient aspect of marker identification from microsatellite-enriched libraries is the proportion of clones with identical sequences. This can substantially increase the number of clones that need to be sequenced in order to identify a sufficient number of microsatellite loci. We propose the use of single-stranded conformation polymorphism (SSCP) analysis to identify unique clones prior to sequencing. We used this approach prior to sequencing from microsatellite-enriched libraries for three marine invertebrate species and were able to obtain a given number of unique clone sequences for only 28% of the sequencing effort that would have been required without SSCP screening.
- Microsatellite enrichment