Molecular evolution of nitrate reductases

The molecular evolution of eucaryotic nitrate reductase (NR) genes was investigated based on published sequence data from fungi, algae and higher plants, and on experimental analysis of grass species NR genes. Extensive variations in NR gene base composition, synonymous codon usage bias and intron number were observed among different lineages. The intron positions are mostly conserved among plants (including algae), while the intron positions between plants and fungi NR genes are completely different. The nonsynonymous substitution rates of NR genes were constant among different lineages, while the overall nucleotide substitution rates varied among some lineages. Based on the nonsynonymous substitution rate, the divergence time of monocots and dicots was estimated to be about 340 Myr using fungi-plant or algae-higher plant divergence times as reference points, and 191 Myr using the rice-barley divergence time as a reference point. These estimates are consistent with other estimates of divergence times based on molecular data. The large difference between these two values appears to be due to the uncertainty of the reference times. It was concluded that NR genes exhibit good molecular clock behavior and may provide a useful model for studying eucaryotic gene evolution.; Most grass species have a single NAD(P)H NR gene copy and two NADH NR gene copies per haploid genome. Notable exceptions are Hordeum vulgare, H. spontaneum and Avena strigosa which have a single NADH NR gene copy. The grass species investigated appear to have at least one NADH NR gene similar to the barley NADH NR gene lacking introns I and III. Comparisons of the barley NADH NR gene heme-hinge region with the two NADH NR genes from Triticum monococcum indicate H. vulgare may have lost one NADH NR gene after the divergence of wheat and barley.