Complete sequence, gene arrangement, and genetic code of mitochondrial DNAof the cephalochordate Branchiostoma floridae (Amphioxus)

We have determined the 15,083-nucleotide (nt) sequence of the mitochondrial DNA (mtDNA) of the lancelet Branchiostoma floridae (Chordata: Cephalochord ata). As is typical in metazoans, the mtDNA encodes 13 protein, 2 rRNA, and 22 tRNA genes. The,gene arrangement differs from the common vertebrate arr angement by only four tRNA gene positions. Three of these are unique to Bra nchiostoma, but the fourth is in a position that is primitive for chordates . It shares the genetic code variations found in vertebrate mtDNAs except t hat AGA = serine, a code variation found in many invertebrate phyla but not in vertebrates (the related codon AGG was not found). Branchiostoma mtDNA lacks a vertebrate-like control region; its largest noncoding region (129 n t) is unremarkable in sequence or base composition, and its location betwee n ND5 and rRNA(G) differs from that usually found in vertebrates. It also l acks a potential hairpin DNA structure like those found in many (though not in all) vertebrates to serve as the second-strand (i.e., L-strand) origin of replication. Perhaps related to this, the sequence corresponding to the DHU arm of tRNA(C) cannot form a helical stem, a condition found in a few o ther vertebrate mtDNAs that also lack a canonical L-strand origin of replic ation. ATG and GTG codons appear to initiate translation in 11 and 2 of the protein-encoding genes, respectively. Protein genes end with complete (TAA or TAG) or incomplete (T or TA) stop codons; the latter are presumably con verted to TAA by post-transcriptional polyadenylation.