Identification of newly settled Caribbean coral recruits by ITS-targeted single-step nested multiplex PCR

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As coral cover has declined throughout the Caribbean, interest in determining the potential for reef recovery via natural recruitment processes has increased. Studies investigating recruitment have been hampered by the difficulty of identifying early stage corals that often lack distinguishing morphological characters. In this study, the utility of targeting the noncoding ribosomal internal transcribed spacer (ITS) regions with a single-step nested multiplex (SSNM) PCR assay to identify common Caribbean coral species was investigated. To design this assay, a database of ITS sequences for 17 common Caribbean coral species was developed. Phylogenies based on the ITS region were generally consistent with current published coral taxonomy and indicated that the ITS regions provided sufficient variability to be useful for distinguishing corals to at least the genus level. Ultimately, we developed ITS-targeted single-step nested multiplex PCR assays capable of differentiating six corals to the species level, two to the genus level, and a pair of coral species that were recently separated at the genus level. This assay was used to classify coral recruits previously identified based on morphological characters. Agreement between these two approaches was low and highlighted the ability of the SSNM-PCR assay to increase the certainty and accuracy of coral recruit identifications. The coral SSNM assay shows promise as an effective method of identifying early stage corals to the genus or species level, and as a valuable tool in studies investigating reef recovery.