Seventy-four Universal Primers for Characterizing the Complete Mitochondrial Genomes of Scleractinian Corals (Cnidaria; Anthozoa)

Use of universal primers designed from a public DNA database can accelerate characterization of mitochondrial (mt) genomes for targeted taxa by polymerase chain reaction (PCR) amplification and direct DNA sequencing. This approach can obtain large amounts of mt information for phylogenetic inferences at lower costs and in less time. In this study, 88 primers were designed from 13 published scleractinian mt genomes, and these were tested on Euphyllia ancora, Galaxea fascicularis, Fungiacyathus stephanus, Porites okinawensis, Goniopora columna, Tubastraea coccinea, Pavona venosa, Oulastrea crispata, and Polycyathus sp., representing 7 families of complex and robust corals. Seventy-four of the 88 primers (84.1%) successfully amplified completed mt genomes of these 9 corals. Several unique features were identified, including a group I intron insertion in the cytochrome oxidase subunit I (COI) genes of Por. okinawensis, Gon. columna, T. coccinea, and F. stephanus and an extended length of the 3'-end of the COI gene of E. ancora. Preliminary tests using a subset of primers successfully obtained the COI 3'-end of Euphyllia representatives, and the resulting species phylogeny is in agreement with corallite characters and tentacle shapes. The universal primers provided herein effectively decoded scleractinian mt genomes, and can be used to reveal different levels of molecular phylogenetic inferences in scleractinian corals.