Variation in Coding (NADH Dehydrogenase Subunits 2, 3, and 6) and Noncoding Intergenic Spacer Regions of the Mitochondrial Genome in Octocorallia (Cnidaria: Anthozoa)

Abstract

Low rates of evolution in cnidarian mitochondrial genes such as COI and 16S rDNA have hindered molecular systematic studies in this important invertebrate group. We sequenced fragments of 3 mitochondrial protein-coding genes (NADH dehydrogenase subunits ND2, ND3 and ND6) as well as the COI-COII intergenic spacer, the longest noncoding region found in the octocoral mitochondrial genome, to determine if any of these regions contain levels of variation sufficient for reconstruction of phylogenetic relationships among genera of the anthozoan subclass Octocorallia. Within and between the soft coral families Alcyoniidae and Xeniidae, sequence divergence in the genes ND2 (539 bp), ND3 (102 bp), and ND6 (444 bp) ranged from 0.5% to 12%, with the greatest pairwise distances between the 2 families. The COI-COII intergenic spacer varied in length from 106 to 122 bp, and pairwise sequence divergence values ranged from 0% to 20.4%. Phylogenetic trees constructed using each region separately were poorly resolved. Better phylogenetic resolution was obtained in a combined analysis using all 3 protein-coding regions (1085 bp total). Although relationships among some pairs of species and genera were well supported in the combined analysis, the base of the alcyoniid family tree remained an unresolved polytomy. We conclude that variation in the NADH subunit coding regions is adequate to resolve phylogenetic relationships among families and some genera of Octocorallia, but insufficient for most species - or population-level studies. Although the COI-COII intergenic spacer exhibits greater variability than the protein-coding regions and may contain useful species-specific markers, its short length limits its phylogenetic utility.

Truncation of subunit ND2 disrupts the threefold symmetry of the antiporter‐like subunits in complex I from higher metazoans

“…Variation in the length of ND2 within the Cnidaria has been noted previously [25][26][27][28]. Following our reclassification of the M. senile sequence, the cnidarian mitochondrial genome sequences were inspected.…”

“…3B is based on the position of the most-upstream initiator codon possible; our evaluation suggests that the short ND2 sequence emerged in a metazoan lineage that directly gave rise to bilaterian animals. Finally, we note that analyzing the phylogenetic relationships between closely related organisms using their mitochondrial DNA and protein sequences has become commonplace; analyses of the phylogenetic relationships amongst Cnidaria based on these approaches (see for example [25][26][27][28]) may have been influenced by discrepancies in the predicted lengths of ND2.…”

Deep-sea octocorals and antipatharians show no evidence of seamount-scale endemism in the NW Atlantic

“…Short sequences (<1000 bp) of mtDNA have not been shown to be variable at the intraspecific level in most anthozoans and therefore are not suitable for population-level studies (France & Hoover 2001, Shearer et al 2002, McFadden et al 2004, but see Chen et al 2008a,b for scleractinians). Nuclear DNA, however, may be more variable than mtDNA in anthozoans (Chen et al 2009).…”

New records of the genera <em>Leptogorgia, Pacifigorgia</em> and <em>Eugorgia</em> (Octocorallia: Gorgoniidae) from Ecuador, with a description of a new species

“…Partial COII-COI (including Igr1 region) and MutS sequences were amplified by PCR using the following primers: COII8068F (McFadden et al 2004), COIOCTR (France and Hoover 2002), the newly developed COI-Gorg1-R3 (5′-AGA-GAAGGTGGTAATAACCAGAAA-3′) and COIGorg2-F2 (5′-GATTCGGAAATTGGTTTGTG-3´) for COI + Igr1; ND42599F (France and Hoover 2002) and MUT3458R (Sánchez et al 2003) for MutS. Amplifications were carried out in a final volume of 50 µL containing 5 µL of 10x buffer (containing 10×2 mM MgCl 2 ), 1 µL dNTPs mix (10 mM), 0.8 µL of each primer (10 µM), 0.5 µL of Taq DNA polymerase (5U/ µL) (Biotools) and 2 µL of genomic DNA.…”