Strategies for amplification by polymerase chain reaction of the complete sequence of the gene encoding nuclear large subunit ribosomal RNA in corals

The nearly complete nuclear large subunit ribosomal RNA (LSU rRNA) gene in corals was amplified by primers designed from polymerase chain reaction (PC R) strategies. The motif of the putative 3'-terminus of the LSU rRNA gene w as sequenced and identified from intergenic spacer (IGS) clones obtained by PCR using universal primers designed for corals. The S'-end primer was con structed in tandem with the universal 5'-end primer for the LSU rRNA gene. PCR fragments of 3500 bp were amplified for octocorals and non-Acropora scl eractinian corals. More than 80% of the Acropora LSU rRNA gene (3000 bp) wa s successfully amplified by modification of the 5'-end of the IGS primer. A nalysis of the 5'-end of LSU rDNA sequences, including the D1 and D2 diverg ent domains, indicates that the evolutionary rate of the LSU rDNA differs a mong these taxonomic groups of corals. The genus Acropora showed the highes t divergence pattern in the LSU rRNA gene, and the presence of a long branc h of the Acropora clade from the other scleractinian corals in the phylogen etic tree indicates that the evolutionary rate of Acropora LSU rDNA might h ave accelerated after divergence from the common ancestor of scleractinian corals.