Employing of the amplified fragment length polymorphism (AFLP) methodology as an efficient population genetic tool for symbiotic cnidarians

Although the use of molecular markers in population genetics of marine organisms is increasingly employed, methodologic limitations still hampered the research for some taxa, such as symbiotic cnidarians, including scleractinian corals. The development of molecular tools in scleractinian corals' studies is faced with a list of obstacles, such as high cost, labor, time consuming, contamination with foreign DNA, and markers with low resolution. The AFLP (amplified fragment length polymorphism) method, overcomes most of the obstacles listed above except of the difficulty of contamination by algal symbiont DNA. We compared the implication of two pre-DNA extraction treatments to obtain coral DNA free of algal contaminations, termed as CPEM, cell population enriched method, and TTEM, total tissue extraction method. The CPEM process result in pure coral DNA for all samples, but is time consuming, whereas in the TTEM process, approximately 25% to 18% of the samples are still contaminated by algal DNA. However, algal DNA contaminations in the PCR at 2.5×10 ^-1 ng level (approximately 100 algal cells) and below, did not amplify any new AFLP band or peak for neither radioactive nor florescence analyses. Therefore, even the TTEM process may be used because it is faster, easier to handle, and easily employed on a large amount of samples, with minimal contamination artifacts. When correctly employed, both methods are applicable to wide experimental manipulations.