Evolution of linear mitochondrial genomes in medusozoan cnidarians

Abstract

In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans.

FIG. 1.—

Compositional properties of cnidarian mitochondrial coding sequences. The total G-C content of mitochondrial protein genes is plotted against the percentage of amino acids encoded by G- and C-rich codons (glycine, alanine, arginine, and proline [G + A + R + P]). The trend line and correlation coefficient are displayed. Hydrozoa are characterized by very A-T rich genomes and relatively fewer [G + A + R + P] codons. Staurozoan have relatively higher GC content similar to anthozoans.

FIG. 2.—

Evolution of mitochondrial genomes in Medusozoa (Cnidaria) based on phylogenetic relationships according to Collins et al. (2006), Collins et al. (2008), and Cartwright et al. (2008). (A) Comparison of mitochondrial gene orders between various medusozoan clades and the putative mitochondrial AMGO. Breaks in contigs mark the ends of linear mitochondrial chromosomes. Genes are transcribed from left to right unless underlined. cox1-p corresponds to the partial copy of cox1 at the end of the mtDNA molecule(s) in the Hydridae family. polB is an inferred member of the B DNA polymerase gene family and ORF314 is an unidentified ORF located upstream of it. Lightning bolts represent breaks in the mitochondrial chromosomes. Black arrows depict directions of inferred genome rearrangements. (B) Evolution of genome organization of the linear mtDNA in Medusozoa. The phylogeny is based on Collins et al. (2006). Major genomic rearrangements are labeled. 1) Linearization of the mtDNA by insertion of a linear plasmid of unknown source; 2) loss of polB and ORF314, and duplication of cox1 at each end of the linear chromosome within Hydrozoa after the divergence of Trachylina; 3) displacement of tRNAs and inversion of rnl in Aplanulata; 4) genome segmentalization of the mtDNA in several Hydridae species with consequent trnM and cox1 duplication; 5) high level segmentalization of the mtDNA in cubozoan; and 6) displacement of trnW in the coronate L. unguiculata.

FIG. 3.—

Consensus secondary structure of tRNAs encoded by the mtDNA of Hydrozoa, Scyphozoa, and Staurozoa. Bold letters with black arrows correspond to position that are missing in some taxa: in ${\text{tRNA}}_{\text{CAU}}^{\text{Met}}$, two nucleotides at positions 16 and 17 of the D-loop in Staurozoa, and positions 1 and 71 in the acceptor stem of the hydrozoan N. bachei; in ${\text{tRNA}}_{\text{UCA}}^{\text{Trp}}$, position 9 of the connector region between the acceptor and the D-arm in the Hydridae family, position 16 of the D-loop in staurozoan and all hydrozoan but the trachyline Cubaia aphrodite, and position 42 of the variable loop in all hydrozoan. Bold letters without arrow correspond to an extra base pair in the anticodon arm of ${\text{tRNA}}_{\text{UCA}}^{\text{Trp}}$ in Hydrozoa and Staurozoa, typical to type 7 tRNAs.

FIG. 4.—

Putative control region and terminal stem-loop found in medusozoan mtDNA. (A) Consensus sequence of the putative control regions (CR) found in the mtDNA of Hydrozoa, Scyphozoa, and Staurozoa. This CR corresponds to the largest IGR that delimits two sets of genes with opposite transcriptional polarity. (B) Putative stem-loop structure found at the end of scyphozoan mtDNA.