The Mitochondrial Genome of Acropora tenuis (Cnidaria; Scleractinia) Contains a Large Group I Intron and a Candidate Control Region

Abstract

The complete nucleotide sequence of the mitochondrial genome of the coral Acropora tenuis has been determined. The 18,338 bp A. tenuis mitochondrial genome contains the standard metazoan complement of 13 protein-coding and two rRNA genes, but only the same two tRNA genes (trnM and trnW) as are present in the mtDNA of the sea anemone, Metridium senile. The A. tenuis nad5 gene is interrupted by a large group I intron which contains ten protein-coding genes and rns; M. senile has an intron at the same position but this contains only two protein-coding genes. Despite the large distance (about 11.5 kb) between the 5?-exon and 3?-exon boundaries, the A. tenuis nad5 gene is functional, as we were able to RT-PCR across the predicted intron splice site using total RNA from A. tenuis. As in M. senile, all of the genes in the A. tenuis mt genome have the same orientation, but their organization is completely different in these two zoantharians: The only common gene boundaries are those at each end of the group I intron and between trnM and rnl. Finally, we provide evidence that the rns-cox3 intergenic region in A. tenuis may correspond to the mitochondrial control region of higher animals. This region contains repetitive elements, and has the potential to form secondary structures of the type characteristic of vertebrate D-loops. Comparisons between a wide range of Acropora species showed that a long hairpin predicted in rns-cox3 is phylogenetically conserved, and allowed the tentative identification of conserved sequence blocks.

Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum

“…1), and compared it with the mtDNA genomes of other diploblasts (15,44,45) and the choanoflagellate Monosiga brevicollis (43). The 43,079-bp circular mtDNA genome of Trichoplax is more than twice the size of the mtDNA found in most metazoans (17-25 kb), including those of poriferans (15,46) and cnidarians (44,45) (Table 1), making it the largest known animal mtDNA genome. The size and composition of the Trichoplax mtDNA genome resembles that of the choanoflagellates and is in striking contrast to the streamlined genomes found in virtually all metazoans.…”

“…Metazoans, on the other hand, have compacted 15-to 20-kb circular mitochondrial genomes that encode a nearly identical set of 12-14 proteins for oxidative phosphorylation and 24-25 structural RNAs (16S rRNA, 12S rRNA, and tRNAs) without significant intragenic spacers and, generally, without introns. Mitochondrial DNA variants exist in metazoans, such as the presence of type I introns and linear mtDNA molecules found in cnidarians (34,44,45), the presence of the atp9 gene in sponges (15,46), and the secondary expansion of mtDNA found in some mollusks (47, 48) and insects (49).Our analysis shows that the Trichoplax mitochondrion possesses the largest known metazoan mtDNA genome, at 43,079 bp, more than twice the size of the typical metazoan mtDNA. Its large size is due not to secondary expansion but to features shared with metazoan outgroups, such as intragenic spacers, several introns, ORFs of unknown function, and protein-coding regions that are generally larger than that found in animals.…”

“…Metazoans, on the other hand, have compacted 15-to 20-kb circular mitochondrial genomes that encode a nearly identical set of 12-14 proteins for oxidative phosphorylation and 24-25 structural RNAs (16S rRNA, 12S rRNA, and tRNAs) without significant intragenic spacers and, generally, without introns. Mitochondrial DNA variants exist in metazoans, such as the presence of type I introns and linear mtDNA molecules found in cnidarians (34,44,45), the presence of the atp9 gene in sponges (15,46), and the secondary expansion of mtDNA found in some mollusks (47,48) and insects (49).…”

Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

“…However, some basal metazoans do exhibit greater variation in mtDNA size and gene content (47). This includes multiple examples of HGT of group I intron sequences (normally not found in animals) into the mtDNA of a sponge (48), a sea anemone (49), and a coral (50).…”

The partial mitochondrial genome of Leiopathes glaberrima (Hexacorallia: Antipatharia) and the first report of the presence of an intron in COI in black corals

“…Over the next several years seven other anthozoans mt genomes were published (Beaton et al 1998;Van Oppen et al 2002;Fukami and Knowlton 2005;Tseng et al 2005). This anthozoan genomic database was completed in 2006 with not less than fourteen new genomes, mainly covering Scleractinia and Corallimorpharia (Medina et al 2006), and in 2007 with the first antipatharian (Brugler and France 2007) and the first zoanthid (Sinniger et al 2007) mt genomes.…”