INTRAGENOMIC, INTRA- AND INTERSPECIFIC VARIATION IN THE RDNA ITS OF PORIFERA REVEALED BY PCR-SINGLESTRAND CONFORMATION POLYMORPHISM (PCR-SSCP)

Abstract

We have applied the polymerase chain reaction-based single-strand conformation polymorphism method (PCR-SSCP) to detect sequence variation in the first and second internal transcribed spacers (ITS1, ITS2) of ribosomal DNA (rDNA). These polymorphic DNA sequences have been used as additional characters to separate species of Cliona Grant, 1826 (Hadromerida) and to estimate levels of variability within and among populations of Hymeniacidon heliophila (Parker, 1910) (Halichondrida). The PCR-SSCP method allowed us to quickly detect different migration patterns of fragments which reflect DNA sequence diversity, both for individuals of different species and for individuals of the same population. We concluded that the PCR-SSCP method is: (1) useful to resolve differences at the species level; (2) simple, of low cost, fast, and non-radioactive; (3) excellent as a fast screening method for species identification, and might thus be a useful tool to discriminate sibling species and detect intragenomic variation without cloning, prior to sequence analysis.