Abstract
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 250 bp 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 available CYB sequence data from scleractinian and other reef-building corals indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.
Highlights
Coral reefs are widely recognized as being important representatives and biogenic harbors of biodiversity (Plaisance et al, 2011)
Aligned coding sequences were evaluated for K2P divergence between the two genomes using PAUP*4.0b10 (Swofford, 2000) as in Shearer & Coffroth (2008); a sliding-window measure of divergence was calculated for 500-bp regions in 25-bp increments along the whole mitochondrial genome
Mapping these reads to the A. humilis mitochondrial genome generated a single contig of 18,667 bp
Summary
Coral reefs are widely recognized as being important representatives and biogenic harbors of biodiversity (Plaisance et al, 2011). This approach has been relatively straightforward and has often relied on a single gene that is both highly variable at silent nucleotide positions as well as highly conserved for amino acid sequence (Folmer et al, 1994; Hebert et al, 2003). This combination allows the sequencing of this gene with universal primers, yet the discovery of tremendous amounts of nucleotide variation that may be used to distinguish taxa. Meyers (2013) showed that using intron regions within the mitochondrial ND5 locus (Concepcion, Medina & Toonen, 2006) could not resolve many species in the genus Agaricia
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