The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA

Abstract

We describe the complete sequence of the 16,596-nucleotide mitochondrial genome of the zebrafish (Danio rerio); contained are 13 protein genes, 22 tRNAs, 2 rRNAs, and a noncoding control region. Codon usage in protein genes is generally biased toward the available tRNA species but also reflects strand-specific nucleotide frequencies. For 19 of the 20 amino acids, the most frequently used codon ends in either A or C, with A preferred over C for fourfold degenerate codons (the lone exception was AUG: methionine). We show that rates of sequence evolution vary nearly as much within vertebrate classes as between them, yet nucleotide and amino acid composition show directional evolutionary trends, including marked differences between mammals and all other taxa. Birds showed similar compositional characteristics to the other nonmammalian taxa, indicating that the evolutionary trend in mammals is not solely due to metabolic rate and thermoregulatory factors. Complete mitochondrial genomes provide a large character base for phylogenetic analysis and may provide for robust estimates of phylogeny. Phylogenetic analysis of zebrafish and 35 other taxa based on all protein-coding genes produced trees largely, but not completely, consistent with conventional views of vertebrate evolution. It appears that even with such a large number of nucleotide characters (11,592), limited taxon sampling can lead to problems associated with extensive evolution on long phyletic branches.

Figure 1

Maximum likelihood estimate of vertebrate phylogeny (−ln likelihood = 239855.997). Likelihood analysis used the GTR + I + Γ model with parameter values estimated from the maximum parsimony tree. This model was significantly better by likelihood ratio test than the Tamura-Nei + I + Γ model (X² = 15,792, d.f. = 3, P < 0.001). The tree shown had significantly greater likelihood for the present data than the generally accepted vertebrate tree, the maximum parsimony tree, and the LogDet distance tree indicated by the Shimodaira–Hasegawa (Shimodaira and Hasegawa 1999) test (P < 0.001 in each case). Scale bar indicates the probability of change per nucleotide site over the branch length interval shown. Lamprey was the designated outgroup.

Figure 2

Variability of nucleotides, amino acids, and hydropathy across the mitochondrial genome. The sequence is of the concatenated protein-coding genes and the bar at top indicates the limits of each gene. The sequence for ND6 is the reverse complement to maintain a consistent reading frame. Plots are the mean values for all 36 vertebrate taxa with a sliding window of 10 for amino acids and third-position nucleotides or 20 for (combined) first- and second-position nucleotides.