The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda)

Abstract

Background: Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although complete mitochondrial genome sequences have been reported for more than 600 animals, the taxonomic sampling is highly biased toward vertebrates and arthropods, leaving much of the diversity yet uncharacterized.

Results: The mitochondrial genome of the bellybutton nautilus, Nautilus macromphalus, a cephalopod mollusk, is 16,258 nts in length and 59.5% A+T, both values that are typical of animal mitochondrial genomes. It contains the 37 genes that are almost universally found in animal mtDNAs, with 15 on one DNA strand and 22 on the other. The arrangement of these genes can be derived from that of the distantly related Katharina tunicata (Mollusca: Polyplacophora) by a switch in position of two large blocks of genes and transpositions of four tRNA genes. There is strong skew in the distribution of nucleotides between the two strands, and analysis of this yields insight into modes of transcription and replication. There is an unusual number of non-coding regions and their function, if any, is not known; however, several of these demark abrupt shifts in nucleotide skew, and there are several identical sequence elements at these junctions, suggesting that they may play roles in transcription and/or replication. One of the non-coding regions contains multiple repeats of a tRNA-like sequence. Some of the tRNA genes appear to overlap on the same strand, but this could be resolved if the polycistron were cleaved at the beginning of the downstream gene, followed by polyadenylation of the product of the upstream gene to form a fully paired structure.

Conclusion: Nautilus macromphalus mtDNA contains an expected gene content that has experienced few rearrangements since the evolutionary split between cephalopods and polyplacophorans. It contains an unusual number of non-coding regions, especially considering that these otherwise often are generated by the same processes that produce gene rearrangements. The skew in nucleotide composition between the two strands is strong and associated with the direction of transcription in various parts of the genomes, but a comparison with K. tunicata implies that mutational bias during replication also plays a role. This appears to be yet another case where polyadenylation of mitochondrial tRNAs restores what would otherwise be an incomplete structure.

Figure 1

Mitochondrial gene map of the cephalopod mollusk Nautilus macromphalus. Genes for proteins and rRNAs are shown with standard abbreviations with an arrow indicating the direction of transcription. Genes for tRNAs are designated by a single letter for the corresponding amino acid, with the two leucine and two serine tRNAs differentiated by numeral (S1, S2, L1, and L2 recognizing codons AGN, UCN, CUN, and UUR, respectively). tRNA genes shown outside the circle are transcribed clockwise and those inside the circle are transcribed counter-clockwise. The largest non-coding region is designated "nc".

Figure 2

Reconstruction of mitochondrial genome rearrangements for Nautilus macromphalus. At the top is the nearly complete gene arrangement for Phoronis architecta [11], a presumed outgroup to the mollusks, shown to polarize two of the cephalopod rearrangements: Having trnP in opposite orientation to nad6 and nad1 is the ancestral condition, as is having trnD between cox2 and atp8. The only two differences between the chiton Katharina tunicata [28] and the two octopus species is the inversion of trnP in the octopus and the transposition of trnD in the chiton. (No attempt is being made here to reconstruct all of the rearrangements between the phoronid and the chiton.) The arrangement found in the N. macromphalus, then, can be reconstructed by the additional switch in order of two large blocks of genes plus transpositions of trnF and trnT. Genes are not drawn to scale and are abbreviated as in Fig. 1 except that underlining signifies right-to-left transcriptional orientation. All genomes are circular and only graphically linearized at an arbitrarily chosen point. These genomes are chosen to illustrate the paucity of rearrangements in these particular lineages. The cuttlefish and several squid with complete mtDNA sequences (see text) have experienced many rearrangements unique to their lineages, and these patterns are reconstructed by Akasaki et al. [31].

Figure 3

Nautilus macromphalus mitochondrial tRNA gene sequences folded into typical cloverleaf structures. Lower case "a" in parentheses indicates likely replacements by (poly)adenylation after transcript cleavage at the downstream tRNA (see text for explanation). Structural features are shown on tRNA(V). Also shown is the secondary structure possible for the repeats in the large non-coding region that appear to be pseudogenes.

Figure 4

Plot of A+C and G+T composition along mtDNAs of Nautilus macromphalus and Katharina tunicata using a sliding window of 100 nucleotides. In each case, the nucleotide composition is being shown for the strand reported, i.e. the one that is the sense strand for cox1. Numbering of nucleotides begins at the arbitrarily chosen cox1 (as in Additional file 4 for N. macromphalus). The scaled gene maps are also presented. tRNA genes are pictured but not labeled. Underlining and light shading indicates opposite, i.e. right-to-left transcriptional orientation. Numerals label each non-coding region larger than 20 nts, which are then projected onto the plot by gray highlighting. Several of these correspond to positions where there is a shift in nucleotide bias. Asterisks beside two of the numerals for K. tunicata indicate some ambiguity where these may instead be supernumerary tRNA genes [28]. Red bars show the major transposition between the two genomes (see Fig. 2).