Mitochondrial gene barcoding of NE Atlantic Octocorals
Mitochondrial gene barcoding is a useful way of identifying unknown specimens; however, their effectiveness in distinguishing between anthozoans remains controversial. It has been demonstrated that anthazoans have unusually slow evolving mitochondrial genomes and therefore lack sufficient variation for differentiation at low taxonomic levels. However, DNA barcodes have proven useful for analysis of scleratinian corals, and studies on the less well known octocorals, a sub-class of anthozoa, have shown some improvements in taxonomic identification with the use of more gene sequences to gain greater phylogenetic resolution. Here we present work on the phylogenetic analysis of octocorals collected throughout the NW Atlantic using three mitochondrial gene barcodes to test the ability of this combination to distinguish between known octocoral species. Octocoral specimens were collected from the Bay of Biscay and waters surrounding the Azores, Ireland, NW Scotland, and Iceland. Total DNA was extracted from samples and each sequenced for three mitochondrial regions: the ND2 subunit of NADH dehydrogenase, the “Folmer region” of COI with an adjacent intergenic region igr1, and the octocoral specific mitochondrial protein coding gene msh1. Phylogenetic reconstruction was performed on 144 samples by combining all three barcode regions and results were compared with morphological identifications of the specimens.
Complete genomes of octocorals (Figueroa 2013)
Bamboo corals have different arrangement of mtdna (Brugler 2008)
CO1 isn't great for corals (France 2002)
General biology of octocorals (Watling 2011)
Collections were made during two cruises in the northeast Atlantic. First in April 2010 using the ROV Holland 1 during cruise CE10014 on the Celtic Explorer (Marine Institute, Ireland). Second in September 2011 using the ROV Victor 6000 during the "BobEco" cruise aboard Pourquoi Pas (Ifremer, France). Additional samples were collected by Fernando Tempera (Azores) and Stefan Ragnarsson (Iceland) and Kirsty Kemp (Scotland) (Wright 2014).
Specimens were identified by Michelle Taylor and Andrea Braga-Henriques.
Subsamples of specimens were stored in 75-95% ethanol. DNA extraction used the DNeasy Tissue kit (QIAGEN Ltd. West Sussex, UK), following the manufacturer’s instructions with the modification of a 48 hour digestion period. PCRs were performed on successful extractions using 20ul reaction volumes consisting of: Xul PCR mastermix (Qiagen ltd), 1ul forward and reverse primers (0.2 pm concentration). Primers used were XXX for mutS, YYY for ND2, and ZZZ for CO1
We sampled X specimens, representing Y taxa for Z regions...
Amy R. Baco, Stephen D. Cairns. Comparing Molecular Variation to Morphological Species Designations in the Deep-Sea Coral Narella Reveals New Insights into Seamount Coral Ranges. PLoS ONE 7, e45555 (2012). Link
Mercer R. Brugler, Scott C. France. The Mitochondrial Genome of a Deep-Sea Bamboo Coral (Cnidaria, Anthozoa, Octocorallia, Isididae): Genome Structure and Putative Origins of Replication Are Not Conserved Among Octocorals. Journal of Molecular Evolution 67, 125-136 (2008). Link
Emily Dolan, Paul A. Tyler, Chris Yesson, Alex D. Rogers. Phylogeny and systematics of deep-sea sea pens (Anthozoa: Octocorallia: Pennatulacea). Molecular Phylogenetics and Evolution 69, 610-618 (2013). Link
Diego F. Figueroa, Amy R. Baco. Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae. Deep Sea Research Part II: Topical Studies in Oceanography (2013). Link
Scott C. France, Loretta L. Hoover. Hydrobiologia 471, 149-155 (2002). Link
S. Herrera, T. M. Shank, J. A. Sánchez. Spatial and temporal patterns of genetic variation in the widespread antitropical deep-sea coral Paragorgia arborea. Molecular Ecology 21, 6053-6067 (2012). Link
CATHERINE S. McFADDEN, YEHUDA BENAYAHU, ERIC PANTE, JANA N. THOMA, P. ANDREW NEVAREZ, SCOTT C. FRANCE. Limitations of mitochondrial gene barcoding in Octocorallia. Molecular Ecology Resources 11, 19-31 (2011). Link
Catherine S. McFadden, Ian D. Tullis, M. Breton Hutchinson, Katherine Winner, Jill A. Sohm. Variation in Coding (NADH Dehydrogenase Subunits 2, 3, and 6) and Noncoding Intergenic Spacer Regions of the Mitochondrial Genome in Octocorallia (Cnidaria: Anthozoa). Marine Biotechnology 6, 516-526 (2004). Link