Mitochondrial genomes from the animal phyla Brachiopoda (Terebratalia transversa), Phoronida (Phoronis architecta), and Chaetognatha (Paraspadella gotoi): Molecular evolution and phylogenetic analyses

The relationships among the animal phyla are not completely resolved. Some taxa are particularly difficult to place in the metazoan tree. Pylogenetic placement of the lophophorate phyla, including the brachiopods and phoronids, and the chaetognaths has been difficult. Mitochondrial DNA (mtDNA) has been shown to contain two useful data sets for phylogenetic analysis: amino acid sequences and gene arrangements. MtDNA can also be used as a model for genome evolution.;MtDNA was amplified using a combination of PCR protocols. The lophophorate mtDNAs were sequenced using a primer walking approach; the chaetognath was sequenced using a combination of primer walking and cloning. The lophophorate sequences were assembled using ABI's Sequence Navigator; the chaetognath was assembled with PHRAP. All gene annotations were performed using MacVector. All phylogenetic analyses were performed using PAUP.;Both the amino acid data and the gene arrangement data resolved the position of the brachiopods and phoronids in the metazoan tree, namely in a group of animals including annelids and mollusks. That these phyla arose in this part of the tree rather than in or near deuterostome animals---as has been previously hypothesized---is significant to our understanding the pattern of evolution of gene networks, particularly developmental programs. The amino acid data also reveal the Chaetognatha to be the sister taxon to the protostome taxa, further informing our understanding of the pattern of animal evolution.;Mutational bias in the brachiopod mtDNA has strongly affected not only codon usage, but amino acid composition as well. The chaetognath genome is very unusual. It contains only one tRNA gene rather than the typical 22, and is missing a protein-encoding gene (atp6) found in all other animal mtDNAs. Its 14 genes are encoded in both strands, but unusually so: all genes encoded in a particular strand are arranged consecutively. There are five genes in one strand, nine in the other. The nine genes are separated from one another by up to a dozen intergenic nucleotides, typical of animal mtDNAs. The other five genes are not separated at all. This suggests that the mRNAs transcribed from the two strands may be processed each in different manner.