Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: Sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa

We report a contiguous region of more than half (>7,500 nt) of the mitochon drial genomes for Platynereis dumerii (Annelida: Polychaeta), Helobdella ro busta (Annelida: Hirudinida), and Galathealinum brachiosum (Pogonophora: Pe rviata). The relative arrangements of all 22 genes identified for Helobdell a and Galathealinum are identical to one another and to their arrangements in the mtDNA of the previously studied oligochaete annelid Lumbricus. In co ntrast, Platynereis differs from these taxa in the positions of several tRN A genes and in having two additional tRNA genes (trnC and trnM) and a large noncoding sequence in this region. Comparisons of relative gene arrangemen ts and of the nucleotide and inferred amino acid sequences among these and other published taxa provide strong support for an annelid-mollusk clade th at excludes arthropods, and for the inclusion of pogonophorans within Annel ida, rather than giving them separate phylum status. Gene arrangement compa risons include the first use of a recently described method on previously u npublished data. Although a variety of alternative initiation codons are ty pically used by mitochondrial protein-encoding genes, ATG appears to be the initiator for all but one reported here. The large noncoding region (1,091 nt) identified in Platynereis has no significant sequence similarity to th e noncoding region of Lumbricus, although each contains runs of TA dinucleo tides and of homopolymers, which could potentially serve as signaling eleme nts. There is strong bias for synonymous codon usage in Helobdella and espe cially in Galathealinum. in this latter taxon, 5 codons are completely unus ed, 13 are used three or fewer times, and G appears at third codon position s in only 26 of the 2,236 codons. Nucleotide composition bias appears to in fluence amino acid composition of the proteins.