Existence of intra-colonial paralogues of the ribosomal internal transcribed spacer (ITS) impedes studies of intra-colonial genetic variation in the scleractinian coral Diploastrea heliopora (Lamark 1816)

Abstract

The implications of intra-colonial genetic variation in corals are relevant to any research that treats within-colony fragments or tissue samples as genetically identical. We used the fast evolving internal transcribed spacer (ITS) gene region to examine genetic structure among polyps within colonies of Diploastrea heliopora, a common and long-lived Indo-Pacific massive coral. Five polyps, 40 cm. apart, were removed from each of nine D. heliopora colonies found on three of Singapore's southern reefs. Based on initial coral sequences we designed ITS primers specific to D. heliopora, producing successful PCR reactions for DNA extracted from eight polyps. From these eight polyps, 43 good quality clonal sequences were obtained. Sequence variations, or paralogues, were observed in clones derived from individual polyps. A parsimony network using 30 non-truncated sequences showed that, even though there appeared to be some grouping of haplotypes in relation to natal reef, occasionally clones from the same polyp were more distantly related to each other than clones from colonies >10 km apart. The presence of high paralogue levels suggests that ITS is not suitable for studies of intra-colonial genetic variation for organisms such as corals where hybridization and other mechanisms may work against concerted evolution to homogenize the ITS sequences. © National University of Singapore.