Complete sequence, gene arrangement, and genetic code of mitochondrial DNA of 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: Cephalochordata). As is typical in metazoans, the mtDNA encodes 13 protein, 2 rRNA, and 22 tRNA genes. The,gene arrangement differs from the common vertebrate arrangement by only four tRNA gene positions. Three of these are unique to Branchiostoma, but the fourth is in a position that is primitive for chordates. It shares the genetic code variations found in vertebrate mtDNAs except that 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 nt) is unremarkable in sequence or base composition, and its location between ND5 and rRNA(G) differs from that usually found in vertebrates. It also lacks 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 other vertebrate mtDNAs that also lack a canonical L-strand origin of replication. 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 converted to TAA by post-transcriptional polyadenylation.