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

The evolutionary history of the order Antipatharia (Cnidaria: Anthozoa: Hexacorallia) as inferred from mitochondrial and nuclear DNA: implications for black coral taxonomy and systematics

“…In terms of IGRs, the most comparable result (in terms of the number of families, genera, and species analysed) at the interfamilial level is the maximum distance reported for the scleractinian nad5 intron (Concepcion et al, 2006), which was 2.15 times higher than the maximum reported in this study [64% (nad5-5′ intron) versus 29.80% (igrN)]. At the intrafamilial level, the maximum distance reported for the octocoral cox1-cox2 IGR (20.4%; McFadden et al, 2004) was most comparable to this study: 20.24% (Aphanipathidae; igrN) and 8.18% (Schizopathidae; igrN). In terms of protein-coding genes, the most comparable result at the interfamilial level is the maximum distance reported for the octocoral msh1 gene: 17.9% (France & Hoover, 2001; this study: 16.18% at cox3-cox1).…”

Exploring the utility of an indel-rich, mitochondrial intergenic region as a molecular barcode for bamboo corals (Octocorallia: Isididae)

“…Although studies of mtDNA variation have reached a mature state in various taxonomic groups, there are still comparatively few studies Marine Genomics 2 (2009) [183][184][185][186][187][188][189][190][191][192] (continued on next page) Keratoisidinae of variation among anthozoans (e.g., Van Oppen et al, 1999;France and Hoover, 2001;McFadden et al, 2004;Smith et al, 2004;Fukami and Knowlton, 2005;Hellberg, 2006). While it is generally accepted that anthozoans have low rates of substitution in mitochondrial genes, most taxa have not been systematically examined, and there is no consensus on the best gene region to use in DNA barcoding studies.…”

“…An alternative barcoding target to mt protein-coding genes in anthozoans are intergenic regions (IGRs), which are typically highly variable in metazoans (e.g., McKnight and Shaffer, 1997;Watanabe et al, 2005;Chen et al, 2008; but see Andolfatto, 2005 andConcepcion et al, 2006), and thus have the potential to reveal increased sequence variation and haplotype diversity, and therefore taxon diversity. Few studies have surveyed IGRs of octocorals for variability and their potential use as taxonomic markers (but see McFadden et al, 2004), possibly because the octocoral mt genomes that have been sequenced contain a relatively low percentage of IGRs, as many genes either overlap or are directly adjacent to one another. Recently, Brugler and France (2008) sequenced the complete mt genome of a novel deep-sea keratoisidin (GenBank accession no.…”

The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: The putative D-loop and a novel ORF of unknown function

“…This scarcity of molecular taxonomic markers for cnidarians is partly explained by the extremely low level of variation observed in their mitochondrial genomes (van Oppen, 1999;France and Hoover, 2002;Shearer et al, 2002;McFadden et al, 2004;Hellberg, 2006), possibly in relation to the presence of proteincoding mitochondrial genes capable of interacting with DNA: a DNA mismatch-repair gene homologous to bacterial mutS is present in octocorallians (Pont-Kingdon et al, 1995, 1998Culligan et al, 2000), a homing endonuclease was described in the plumose anemone Metridium senile (Beagley et al, 1998) and in the zoanthid Savalia savaglia (Sinniger et al, 2007), and a putative DNA-dependant DNA polymerase has recently been found in the mitochondrial genome of the scyphozoan jellyfish Aurelia aurita (Shao et al, 2006). Unusual protein-coding mitochondrial genes are also present in sponges, but all those described until now appear to have metabolic roles, not to interact with DNA (Lavrov et al, 2005;Erpenbeck et al, 2007;Wang and Lavrov, 2007).…”