Multiplexed pyrosequencing of nine sea anemone (Cnidaria: Anthozoa: Hexacorallia: Actiniaria) mitochondrial genomes

Abstract

Six complete and three partial actiniarian mitochondrial genomes were amplified in two semi-circles using long-range PCR and pyrosequenced in a single run on a 454 GS Junior, doubling the number of complete mitogenomes available within the order. Typical metazoan mtDNA features included circularity, 13 protein-coding genes, 2 ribosomal RNA genes, and length ranging from 17,498 to 19,727 bp. Several typical anthozoan mitochondrial genome features were also observed including the presence of only two transfer RNA genes, elevated A + T richness ranging from 54.9 to 62.4%, large intergenic regions, and group 1 introns interrupting NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit I, the latter of which possesses a homing endonuclease gene. Within the sea anemone Alicia sansibarensis, we report the first mitochondrial gene order rearrangement within the Actiniaria, as well as putative novel non-canonical protein-coding genes. Phylogenetic analyses of all 13 protein-coding and 2 ribosomal genes largely corroborated current hypotheses of sea anemone interrelatedness, with a few lower-level differences.

The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep‐sea environment

“…was biased toward A and T , and the overall A + T content was 60.51%. Similar results have also been observed in other actiniarian mitogenomes (Foox et al., ; Zhang & Zhu, ). As is commonly found in metazoan mitogenomes, the A + T content varied in different regions (Table ).…”

“…() observed two ORFs (orfA‐51 and orfB‐26) of unknown function in the mitogenome of the cold‐water sea anemone U. eques , and a truncated version of orfA was also found in tropical reef A. pulchella and cold‐water H. digitate mitogenome. Foox, Brugler, Siddall, & Rodríguez () also observed homologous ORFs in other actinioidean species, but no obvious similarity was noted within the ORFs. Instead of the ORFs described above, two new truncated ORFs (ORFC and ORFD) were observed in the Bolocera sp.…”

“…The A + T content of the mitogenome is extremely high in insects and nematodes and lower in vertebrates (Saccone, Giorgi, Gissi, Pesole, & Reyes, 1999). In the anthozoan mitogenome, the A + T content ranges from 54.9% to 68.1% (Brugler & France, 2007;Foox et al, 2016). The nucleotide composition of the H-strand in Bolocera sp.…”

Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements

“…The HEG, which covers most of the intron sequences (including the ribozyme encoded parts), is fused in-frame with the 5 0 COI exon. Highly expressed in-frame HEGs are observed in the sea anemones Urticina and Bolocera [12], and similar in-frame organizations appear common in other sea anemones such as Isosicyonis, Phymanthus, Actinia, and Stichodactyla ( [15,46,47]; our unpublished results). A COI fusion strategy for intron HEG expression in mitochondria, however, is not unique to sea anemones since several fungi are using this approach [44,48].…”

Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa)

“…Species from the cnidarian class Anthozoa (the clade containing reef-building corals, sea anemones, soft corals, and their relatives) possess relatively large, circular mitochondrial genomes in which protein-coding genes are interspaced with intergenic regions (IGRs) that might play a role in mitochondrial mRNA maturation (e.g. 18,19 ). The mt genome in the cnidarian subphylum Medusozoa (e.g.…”