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There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of all available Scleractinian CYB sequence data indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.
This is an updated version of manuscript submitted on July 1; the only changes are minor formatting changes and inclusion of 2 missing references.
Aligned Cyt B of Scleractinian corals
Nexus formatted sequence alignment of cytochrome b reads from Scleractinian corals, obtained from Genbank. Individual accession numbers associated with each sequence.