The Mitochondrial Genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) Supports Intramolecular Recombination as the Primary Mechanism of Gene Rearrangement in Octocoral Mitochondrial Genomes

Abstract

Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene content and nucleotide composition are, however, identical to most other octocorals, and the additional length is due to the presence of two large, noncoding intergenic regions. Relative to the presumed ancestral octocoral gene order, in P. aldersladei a block of three protein-coding genes (nad6–nad3–nad4l) has been translocated and inverted. Mapping the distribution of mt gene arrangements onto a taxonomically comprehensive phylogeny of Octocorallia suggests that all of the known octocoral gene orders have evolved by successive inversions of one or more evolutionarily conserved blocks of protein-coding genes. This mode of genome evolution is unique among Metazoa, and contrasts strongly with that observed in Hexacorallia, in which extreme gene shuffling has occurred among taxonomic orders. Two of the four conserved gene blocks found in Octocorallia are, however, also conserved in the linear mt genomes of Medusozoa and in one group of Demospongiae. We speculate that the rate and mechanism of gene rearrangement in octocorals may be influenced by the presence in their mt genomes of mtMutS, a putatively active DNA mismatch repair protein that may also play a role in mediating intramolecular recombination.

Niche divergence by deep‐sea octocorals in the genus Callogorgia across the continental slope of the Gulf of Mexico

“…We also included cox1 and 28S of the hexacoral Antipathes atlantica, as an outgroup. Because gene trees were highly congruent among this study (Figs S1 and S2, Supporting information) and others (Brockman & McFadden ; McFadden & van Ofwegen ; Pante et al . ), the genes were concatenated into a 2309‐bp alignment.…”

“…S1‐S3, Supporting information). Taxa were selected based on inclusion in clades throughout the larger Calcaxonia‐Scleraxonia‐Pennatulacea clade (as per Brockman & McFadden ; McFadden & van Ofwegen ; Pante et al . ).…”

Syllidae mitochondrial gene order is unusually variable for Annelida

“…Instead, a transposition mechanism involving recombination with double-stranded break repair is hypothesized. This mechanism would be an example of intramolecular recombination, which among others has been already demonstrated for cnidarians (Brockman and McFadden 2012) and bird mitochondrial genomes (Sammler et al 2011). In some studies the presence of so-called minicircles containing fragments of the mitochondrial genomes coincide with a largely rearranged gene order of the mitochondrium.…”

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

“…One reason for this is that the rate of octocoral mitochondrial gene evolution is very slow. It is estimated to be 10-100× slower than in other metazoans (Chen et al 2009, Brockman andMcFadden 2012), resulting in insufficient resolution to discriminate species within many genera (Sánchez et al 2003, Lepard 2003in Cairns and Bayer 2005. Specimens identified as different morphospecies can share the same barcode, which should motivate additional taxonomic work to test species boundaries and quantify intraspecific morphological and molecular variation (McFadden et al 2010).…”