A comparison of cytochrome b and DNA hybridization data bearing on the phylogeny of swallows (Aves: Hirundinidae)

Cytochrome b sequence data from 17 species representing 16 genera of swallows (Aves: Hirundinidae) were compared with DNA-DNA hybridization data from the same species in a taxonomic congruence assessment of swallow phylogeny. In the process, subsets (partitions) of the cytochrome b sequence data were examined in light of the DNA hybridization distances to assess their potential phylogenetic informativeness. When the sequence data were weighted-with or without reference to the DNA hybridization data-they produced parsimony and maximum likelihood (but not distance) trees that were largely congruent with the DNA hybridization tree. To this extent, the cytochrome b data supported many of the phylogenetic conclusions based on the DNA hybridization tree and vice versa. However, the cytochrome b data produced largely unresolved trees when branch robustness was tested by bootstrapping and other methods. This poor resolution appeared to be caused by a lack of hierarchical structure in the cytochrome b distances, which were confined to a narrow range (between 10-13%), compressed by saturation, and noisy. Partition analysis by codon sites and protein domains yielded typical avian cytochrome b patterns, except for idiosyncrasies attributable to the genetic divergence level of swallows in comparison to other groups of birds whose cytochrome b sequences have been analyzed.     

Nucleotide sequence and evolution of the rat mitochondrial cytochrome b gene containing the ochre termination codon

The nucleotide sequences of the genes for cytochrome b and three potential transfer RNAs (tRNAPro, tRNAThr and tRNAGlu) in cloned rat mitochondrial DNA were determined. The derived amino acid sequence of the cytochrome b protein from the light strand indicated that the C-terminal amino acid is asparagine and the ochre termination codon is encoded in the DNA, in contrast to the the lack of termination codon in the reading frame of human [Anderson et al., Nature 290 (1981) 457] or mouse [Bibb et al., Cell 26 (1981) 167] mitochondrial DNA. The first ATG codon of the cytochrome b gene was spaced five nucleotides from the 5'-end of the tRNAGlu gene on the heavy strand. There was a single nucleotide spacing between the termination codon of the cytochrome b gene and the 5' end of the tRNAThr gene in the light strand. There was also a single nucleotide spacing between the 3'-end of the tRNAThr gene and the 3'-end of the tRNAPro gene on the heavy strand. The amino acid and nucleotide sequences of the cytochrome b genes of mammals and yeast [Nobrega and Tzagoloff, J. Biol. Chem. 255 (1980) 9828] were compared to reveal structural differences in two very different species. At the same time, amino acid substitutions in particular regions of the mammalian gene corresponding to the exon-intron boundaries in the yeast gene were noted. These genetic features are discussed in relation to the extreme compression of genetic information in the mammalian mitochondrial genome as related to the evolution of the gene organization and its sequence.     

Molecular phylogeny of the springhare, Pedetes capensis, based on mitochondrial DNA sequences

The phylogenetic position of the Pedetidae, represented by a single species Pedetes capensis, is controversial, reflecting in part the retention of both Hystricomorphous and Sciurognathous characteristics in this rodent. In an attempt to clarify the species evolutionary relationships, mtDNA gene sequences from 10 rodent species (representing seven families) were analyzed using phenetic, parsimony, and maximum-likelihood methods of phylogenetic inference; the rabbit, Oryctolagus cuniculus (Order Lagomorpha), and cow, Bos taurus (Order Artiodactyla), were used as outgroups. Investigation of 714 base pairs of the protein-coding cytochrome b gene indicate strong base bias at the third codon position with significant rate heterogeneity evident between the three structural domains of this gene. Similar analyses conducted on 816 base pairs of the 12S rRNA gene revealed a transversion bias in the loop sections of all taxa. The cytochrome b gene sequences proved useful in resolving associations between closely related species but failed to produce consistent tree topologies at the family level. In contrast, phylogenetic analysis of the 12S rRNA gene resulted in strong support for the clustering of Pedetidae/Heteromyidae/Geomyidae and Muridae in one clade to the exclusion of the Hystricidae/Thryonomyidae and Sciuridae, a finding which is concordant with studies of rodent fetal membranes as well as reproductive and other anatomical features.      

Cytochrome oxidase subunit II gene in mitochondria of Oenothera has no intron

The cytochrome oxidase subunit II gene has been localized in the mitochondrial genome of Oenothera berteriana and the nucleotide sequence has been determined. The coding sequence contains 777 bp and, unlike the corresponding gene in Zea mays, is not interrupted by an intron. No TGA codon is found within the open reading frame. The codon CGG, as in the maize gene, is used in place of tryptophan codons of corresponding genes in other organisms. At position 742 in the Oenothera sequence the TGG of maize is changed into a CGG codon, where Trp is conserved as the amino acid in other organisms. Homologous sequences occur more than once in the mitochondrial genome as several mitochondrial DNA species hybridize with DNA probes of the cytochrome oxidase subunit II gene.     

Molecular analysis off the phylogeny off 11 genera off the Corvidae

Phylogenetic analysis of 11 genera of Corvidae has been undertaken using a sequence of 925 bp of the cytochrome b gene of the mtDNA. Both maximum-parsimony and maximum-likelihood analyses were performed, and different weighting schemes have been used according to the saturation observed in the data (mostly at the third codon position). The cytochrome b data provide good evidence for the monophyly of the Corvidae, including the Piapiac Ptilostomus afer in spite of its aberrant morphology. In all analyses, the choughs are the first lineage emerging in the family; this result conflicts with the traditional chough-crow group, as well as the hypothesis of the ancestral position of the jays. The monophyly of the American jays is well supported by the molecular data, unlike the Palearctic jays, which are not closely related. The other intergeneric relationships are not strongly supported by bootstrap proportions, and are not congruent in all different weightings and methods, except for groups of species of the same or very closely related genera.     

Relative patterns and rates of evolution in heron nuclear and mitochondrial DNA

Mitochondrial cytochrome b sequence data from 15 species of herons (Aves: Ardeidae), representing 13 genera, were compared with DNA hybridization data of single-copy nuclear DNA (scnDNA) from the same species in a taxonomic congruence assessment of heron phylogeny. The two data sets produced a partially resolved, completely congruent estimate of phylogeny with the following basic structure: (Tigrisoma, Cochlearius, (((Zebrilus, (Ixobrychus, Botaurus)), (((Ardea, Casmerodius), Bubulcus), ((Egretta thula, Egretta caerulea, Egretta tricolor), Syrigma), Butorides, Nycticorax, Nyctanassa)))). Because congruence indicated similar phylogenetic information in the two data sets, we used the relatively unsaturated DNA hybridization distances as surrogates of time to examine graphically the patterns and rates of change in cytochrome b distances. Cytochrome b distances were computed either from whole sequences or from partitioned sequences consisting of transitions, transversions, specific codon site positions, or specific protein-coding regions. These graphical comparisons indicated that unpartitioned cytochrome b has evolved at 5-10 times the rate of scnDNA. Third-position transversions appeared to offer the most useful sequence partition for phylogenetic analysis because of their relatively fast rate of substitution (two times that of scnDNA) and negligible saturation. We also examined lineage-based rates of evolution by comparing branch length patterns between the nuclear and cytochrome b trees. The degree of correlation in corresponding branch lengths between cytochrome b and DNA hybridization trees depended on DNA sequence partitioning. When cytochrome b sequences were not partitioned, branch lengths in the cytochrome b and DNA hybridization trees were not correlated. However, when cytochrome b sequences were reduced to third-position transversions (i.e., unsaturated, relatively fast changing data), branch lengths were correlated. This finding suggests that lineage-based rates of DNA evolution in nuclear and mitochondrial genomes are influenced by common causes.     

Novel primers for complete mitochondrial cytochrome b gene sequencing in mammals

Sequence-based species identification relies on the extent and integrity of sequence data available in online databases such as GenBank. When identifying species from a sample of unknown origin, partial DNA sequences obtained from the sample are aligned against existing sequences in databases. When the sequence from the matching species is not present in the database, high-scoring alignments with closely related sequences might produce unreliable results on species identity. For species identification in mammals, the cytochrome b (cyt b) gene has been identified to be highly informative; thus, large amounts of reference sequence data from the cyt b gene are much needed. To enhance availability of cyt b gene sequence data on a large number of mammalian species in GenBank and other such publicly accessible online databases, we identified a primer pair for complete cyt b gene sequencing in mammals. Using this primer pair, we successfully PCR amplified and sequenced the complete cyt b gene from 40 of 44 mammalian species representing 10 orders of mammals. We submitted 40 complete, correctly annotated, cyt b protein coding sequences to GenBank. To our knowledge, this is the first single primer pair to amplify the complete cyt b gene in a broad range of mammalian species. This primer pair can be used for the addition of new cyt b gene sequences and to enhance data available on species represented in GenBank. The availability of novel and complete gene sequences as high-quality reference data can improve the reliability of sequence-based species identification.     

Sequence evolution and phylogenetic signal in control-region and cytochrome b sequences of rainbow fishes (Melanotaeniidae)

The nucleotide sequences of segments of the cytochrome b gene (351 bp), the tRNA(Pro) gene (49 bp), and the control region (approximately 313 bp) of mitochondrial DNA were obtained from 26 fish representing different populations and species of Melanotaenia and one species of Glossolepis, freshwater rainbow fishes confined to Australia and New Guinea. The purpose was to investigate relative rates and patterns of sequence evolution. Overall levels of divergence were similar for the cytochrome b and tRNA control-region sequences, both ranging from < 1% within subspecies to 15%-19% between genera. However, the patterns of sequence evolution differed. For the cytochrome b gene, transitions consistently exceeded transversions, the bias ranging from 4.2:1 to 2:1, depending on the level of sequence divergence. However, in the control-region sequence, a bias toward transitions (2:1) was observed only in comparisons between very similar sequences, and transversions outnumbered transitions in comparisons of divergent sequences. Graphic comparisons suggested that the control region was saturated for transitions at relatively low levels of sequence divergence but accumulated transversions at a greater rate than did the cytochrome b sequence. These distinct patterns of base substitution are associated with differences in A+T content, which is 70% for the tRNA control- region segment versus 50% for cytochrome b. A test for skewness in the distribution of lengths of random trees indicated that both segments contained phylogenetic signal. Parsimony analyses of the data from the two regions, with or without weighting schemes appropriate to the respective patterns of sequence evolution, identified the same five groupings of sequences, but the relationships among the groups differed. However, in most cases the branches uniting different combinations of groups were poorly supported, and the differences among topologies were insignificant. Considering the observed patterns of base substitution and the results of the phylogenetic analyses, we deduce that both the control region and cytochrome b are appropriate for population genetic studies but that the control region is less effective than cytochrome b for resolving relationships among divergent lineages of rainbow fishes.      

两种(鱼尝)科鱼类在长江和珠江流域Cytb基因序列变异性分析

采用PCR技术获得了长江和珠江流域的两种鲿科鱼类1137bp Cytb基因的片段,进行了序列测定,并用Mega软件进行了序列分析。研究发现两种鲿科鱼类的全序列从第十位碱基起有一个三联体密码子的缺失,推测为鲇形目鱼类Cytb序列所特有特征。黄颡鱼和大鳍鳠种群间的序列差异分别为0．4％和1．6％,介于一般淡水鱼类mtDNA种内序列的变异范围,而高于洄游鱼类序列变异。黄颡鱼属和鲮属Cytb基因序列间的差异为17．6％-18．0％,大大高于种间的序列差异率,也从分子水平上证实了二者属级分类单元的有效性。依据分子进化速率推测,长江和珠江两水系间大鳍鳠的分歧时间为距今27万年左右的更新世中晚期,黄颡鱼的分歧时间在距今7万年左右的更新世末期。推测造成二者有着不同分歧时间的可能原因是：大鳍鳠属暖水性鱼类,在第四纪冰川期间,由于全球性气候变冷,大鳍鳠退至长江以南,并在各水系间产生隔离,各自独立分化至今。而黄颡鱼具有很强的适应性,在第四纪数次冰川期间可能进行过广泛的交流。     

板角山羊mtDNA Cyt b基因变异特点及系统进化研究

测定了板角山羊品种13个个体的细胞色素b基因全序列(1140 bp),比较分析了群体中细胞色素b基因的碱基组成和序列间碱基的变异情况,结果显示:在该品种(群体)中细胞色素b基因序列中6个变异位点上观察到11次T-C间和2次A-G间的碱基转换,除了有2次T-C间碱基转换发生在密码子第2位点为非同义突变以外,其余的11次碱基转换发生在密码子第3位点,均为同义突变;有1次T-G间碱基颠换发生在密码子第2位点,为非同义突变;观察到5种单倍型,单倍型多样度为0.8077.并以绵羊为外群,与山羊属其他种的同源区序列构建系统发生树.结果显示, 在系统地位上板角山羊与胃石山羊有较近的亲缘关系.     

Influence of intercodon and base frequencies on codon usage in filarial parasites

Base frequency, codon usage, and intercodon identity were analyzed in five filarial parasite species representing five Onchocercidae genera. Wucheria bancrofti, Brugia malayi, Onchocerca volvulus, Acanthocheilonema viteae, and Dirofilaria immitis gene sequences were downloaded from NCBI, and analysis was performed using locally designed computer programs and other freely available applications. A clear sequence bias was observed among the nematode species examined. At the nucleotide level, AT basepairs were present in gene sequences at higher frequencies than GC. In addition, codons ending in A or T were used proportionately more than those with G or C in the third-codon position. In addition, the amino acids used most often corresponded to codons ending in AT basepairs. Intercodon base proportion was biased in that A was found most often at N4, second only to T in certain specific cases. Since all of these sequence biases were observed in a relatively consistent fashion among all of the organisms studied, we conclude that sequence bias is a genetic characteristic, which is associated with multiple filarial genera.     

Evolution of the mitochondrial cytochrome oxidase II gene among 10 orders of insects.

We examine the complete nucleotide sequences of the mitochondrial cytochrome oxidase II gene of 13 species of insects, representing 10 orders. The genes range from 673 to 690 bp in length, encoding 226 to 229 amino acids. Several insertion or deletion events, each involving one or two codons, can be observed. The 3' end of the gene is extremely variable in both length and sequence, making alignment of the ends unreliable. Using the first 639 nucleotide positions, for which unambiguous alignments could be obtained, we examine the neighbor-joining trees based on nucleotide divergences and based on conserved subsets of that data, including transversion and amino acid and second codon position divergences. Each of these subsets produces different trees, none of which can be easily reconciled with trees constructed using morphology and the fossil record. Bootstrap analysis using second codon positions strongly supports affinities between the order Blatteria (cockroaches) and the order Isoptera (termites) and between a wasp and the published honeybee sequence (Order Hymenoptera). The divergence of insect orders is very ancient and may have occurred too rapidly for easy resolution using mitochondrial protein sequences. Unambiguous resolution of insect orders will probably require analysis of many additional taxa, using the COII gene and other conserved sequences.     

Gene structure and nucleotide sequence for rat cytochrome P-450c

Two clones from rat genomic libraries that contain the entire gene for rat cytochrome P-450c have been isolated. lambda MC4, the first clone isolated from an EcoR1 library, contained a 14-kb insert. A single 5.5-kb EcoR1 fragment from lambda MC4, the EcoR1 A fragment, hybridized to a partial cDNA clone for the 3' end of the cytochrome P-450c mRNA. This fragment was sequenced using the dideoxynucleotide chain termination methodology with recombinant M13 bacteriophage templates. Comparison of this sequence with the complete cDNA sequence of cytochrome P-450MC [Yabusaki et al. (1984) Nucleic. Acids Res. 12, 2929-2938] revealed that the EcoR1 A fragment contained the entire cytochrome P-450c gene with the exception of a 90-bp leader sequence. The gene sequence is in perfect agreement with the cDNA sequence except for two bases in exon 2. A second genomic clone, lambda MC10, which was isolated from a HaeIII library, contains the missing leading sequence as well as 5' regulatory sequences. The entire gene is about 6.1 kb in length with seven exons separated by six introns, all of the intron/exon junctions being defined by GT/AG. Amino- and carboxy-terminal information are contained in exons 2 and 7, respectively. These exons contain the highly conserved DNA sequences that have been observed in other cytochrome P-450 species. Potential regulatory sequences have been located both 5' to the gene as well as within intron I. A comparison of the coding information for cytochrome P-450c with the sequence of murine cytochrome P3-450 and rat cytochrome P-450d revealed a 70% homology in both the DNA and amino acid sequence, suggesting a common ancestral gene. Genomic blot analyses of rat DNA indicated that the 3-methylcholanthrene-inducible family of cytochrome P-450 isozymes is more limited in number compared to the phenobarbital-inducible isozymes. Cross-hybridization studies with human DNA suggest a high degree of conservation between rat cytochrome P-450c and its human homolog although gross structural differences do exist between the two genes.     

Evolution of the mitochondrial DNA cytochrome b gene in Tetraonidae birds

Mitochondrial fragments containing the cytochrome b gene (1020 bp in size) of four bird species belonging to four genera of the family Tetraonidae (Tetrao parvirostris, Bonasa umbellus, Lagopus lagopus scoticus, and Falcipennis falcipennis) were directly sequenced. Of the 1020 nucleotide positions, 186 were variable and uniformly distributed over the gene and only 46 were parsimony informative. Most substitutions were synonymous. Replacement substitutions were detected for 15 out of 340 amino acid sites; only four replacements were parsimony informative. The greatest codon bias was found for leucine and serine. The C-T transitions and the G-C transversions were, respectively, the most common (60.7%) and the most rare (5.9%). The mutation frequencies were high at the third codon position (85.2%) and relatively low at the first and the second position. At the third codon position of the species examined, the guanine content was the lowest (3.3%) and the cytosine content was the highest (44.5%). Based on the cytochrome b gene sequences, phylogenetic relationships in the order Galliformes are inferred.     

Bayesian estimation of post-Messinian divergence times in Balearic Island lizards

Phylogenetic relationships and timings of major cladogenesis events are investigated in the Balearic Island lizards Podarcislilfordi and P.pityusensis using 2675bp of mitochondrial and nuclear DNA sequences. Partitioned Bayesian and Maximum Parsimony analyses provided a well-resolved phylogeny with high node-support values. Bayesian MCMC estimation of node dates was investigated by comparing means of posterior distributions from different subsets of the sequence against the most robust analysis which used multiple partitions and allowed for rate heterogeneity among branches under a rate-drift model. Evolutionary rates were systematically underestimated and thus divergence times overestimated when sequences containing lower numbers of variable sites were used (based on ingroup node constraints). The following analyses allowed the best recovery of node times under the constant-rate (i.e., perfect clock) model: (i) all cytochrome b sequence (partitioned by codon position), (ii) cytochrome b (codon position 3 alone), (iii) NADH dehydrogenase (subunits 1 and 2; partitioned by codon position), (iv) cytochrome b and NADH dehydrogenase sequence together (six gene-codon partitions), (v) all unpartitioned sequence, (vi) a full multipartition analysis (nine partitions). Of these, only (iv) and (vi) performed well under the rate-drift model. These findings have significant implications for dating of recent divergence times in other taxa. The earliest P.lilfordi cladogenesis event (divergence of Menorcan populations), occurred before the end of the Pliocene, some 2.6Ma. Subsequent events led to a West Mallorcan lineage (2.0Ma ago), followed 1.2Ma ago by divergence of populations from the southern part of the Cabrera archipelago from a widely-distributed group from north Cabrera, northern and southern Mallorcan islets. Divergence within P.pityusensis is more recent with the main Ibiza and Formentera clades sharing a common ancestor at about 1.0Ma ago. Climatic and sea level changes are likely to have initiated cladogenesis, with lineages making secondary contact during periodic landbridge formation. This oscillating cross-archipelago pattern in which ancient divergence is followed by repeated contact resembles that seen between East-West refugia populations from mainland Europe.     

Mitochondrial Genetics of Chlamydomonas Reinhardtii: Resistance Mutations Marking the Cytochrome B Gene

We describe the genetic and molecular analysis of the first non-Mendelian mutants of Chlamydomonas reinhardtii resistant to myxothiazol, an inhibitor of the respiratory cytochrome bc1 complex. Using a set of seven oligonucleotide probes, restriction fragments containing the mitochondrial cytochrome b (cyt b) gene from C. reinhardtii were isolated from a mitochondrial DNA library. This gene is located adjacent to the gene for subunit 4 of the mitochondrial NADH-dehydrogenase (ND4), near one end of the 15.8-kb linear mitochondrial genome of C. reinhardtii. The algal cytochrome b apoprotein contains 381 amino-acid residues and exhibits a sequence similarity of about 59% with other plant cytochrome b proteins. The cyt b gene from four myxothiazol resistant mutants of C. reinhardtii was amplified for DNA sequence analysis. In comparison to the wild-type strain, all mutants contain an identical point mutation in the cyt b gene, leading to a change of a phenylalanine codon to a leucine codon at amino acid position 129 of the cytochrome b protein. Segregation analysis in tetrads from reciprocal crosses of mutants with wild type shows a strict uniparental inheritance of this mutation from the mating type minus parent (UP-). However, mitochondrial markers from both parents are recovered in vegetative diploids in variable proportions from one experiment to the next for a given cross. On the average, a strong bias is seen for markers inherited from the mating type minus parent.     

The molecular evolution of cytochrome c in eukaryotes

Summary Using many more cytochrome sequences than previously available, we have confirmed: 1, the eukaryotic cytochromes c diverged from a common ancestor; 2, the ancestral eukaryotic cytochrome c was not greatly different in character from those present today; 3, fixations are non-randomly distributed among the codons, there being evidence for at least four classes of variability; 4, there are similar classes of variability when the data are considered according to the nucleotide position within the codon; 5, the number of covarions (concomitantly variable codons) in mammalian cytochrome c genes is about 12 and the same value has been obtained for dicotyledonous plants as well; 6, all of the hyper- and most highly variable codons are for external residues, nearly 60 per cent of the invariable codons are for internal residues and nearly half of the codons for internal residues are invariable; 7, the first nucleotide position of a codon is more likely and the second position less likely to fix mutations than would be expected on the basis of the number of ways that alternative amino acids can be reached; 8, the character of nucleotide replacements is enormously non-random, with GA interchanges representing 42% of those observed in the first nucleotide position, but the observation does not stem from a bias in the DNA strand receiving the mutation, nor from the presence of a compositional equilibrium, nor from a bias in the frequency with which different nucleotides mutate, but rather from a bias in the acceptability of an alternative nucleotide as circumscribed by the functional acceptability of the new amino acid encoded; and 9, the unit evolutionary period is approximately 150 million years/observable (amino acid changing) nucleotide replacement/cytochrome c covarion in two diverging lines.Wherever non-randomness has been observed, it has always been consistent with the consideration that an alternative amino acid at any location is more likely to be acceptable the more closely it resembles the present amino acid in its physico-chemical properties.Finally, in no case did the a priori assumption of a biologically realistic phylogeny lead to any observations or conclusions that were in any way significantly different from those obtained when the phylogeny was based solely upon the sequences, proving that the earlier results were not a consequence of some internal circularity.     

Structure and evolution of the avian mitochondrial control region

The structural and evolutionary characteristics of the mitochondrial control region were studied by using control region sequences of 68 avian species. The distribution of the variable nucleotide positions within the control region was found to be genus specific and not dependant on the level of divergence, as suggested before. Saturation was shown to occur at the level of divergence of 10% in pairwise comparisons of the control region sequences, as has also been reported for the third codon positions in ND2 and cytochrome b genes of mtDNA. The ratio of control region vs cytochrome b divergence in pairwise comparisons of the sequences was shown to vary from 0.13 to 21.65, indicating that the control region is not always the most variable region of the mtDNA, but also that there are differences in the rate of divergence among the lineages. Only two of the conserved sequence blocks localized earlier for other species, D box and CSB-1, were found to show a considerable amount of sequence conservation across the avian and mammalian sequences. Additionally, a novel avian-specific sequence block was found.     

Gene structure of a major form of phenobarbital-inducible cytochrome P-450 in rat liver

The gene structure of cytochrome P-450b, a major form of phenobarbital-inducible cytochrome P-450 in rat livers was elucidated by sequence analysis of the cloned genomic DNAs and was compared with the previously determined gene structures of cytochrome P-450e, a minor form of phenobarbital-inducible cytochrome P-450 and two forms of 3-methylcholanthrene-inducible cytochrome P-450 (P-450c and -d). The gene for cytochrome P-450b is 23 kilobase pairs (kb) long and is separated into 9 exons by 8 intervening sequences. This gene structure is very similar to that of cytochrome P-450e except for the first intron, the first intron being much longer in cytochrome P-450b gene (approximately 12 kb) than in cytochrome P-450e gene (3.2 kb), but differs greatly from the gene structures of two 3-methylcholanthrene-inducible cytochrome P-450s as pointed out previously (Sogawa, K., Gotoh, O., Kawajiri, K. & Fujii-Kuriyama, Y. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 5066-5070). The nucleotide sequences in all 9 exons and their flanking regions in introns show very close homology between the two phenobarbital-inducible cytochrome P-450 genes. Forty base substitutions are found in approximately 1900 nucleotides of all exonic sequences, and 15 of them result in 14 amino acid replacements. These base substitutions occur in relatively limited regions of the gene sequences. Most of them are found in exons 6, 7, 8, and 9, most frequently in exon 7 as described previously (Mizukami, Y., Sogawa, K., Suwa, Y., Muramatsu, M. & Fujii-Kuriyama, Y. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 3958-3962). The close sequence homology between the two phenobarbital-inducible cytochrome P-450 genes is also found to extend to the promoter region with one notable exception. The simple repeated sequences of (CA)n which is present at -254 position in cytochrome P-450e gene is also observed at the equivalent position in cytochrome P-450b gene, but the repetitiveness is greatly reduced in cytochrome P-450b gene ((CA)5 for P-450b versus (CA)19 for P-450e), and this may somehow be related to the difference in the level of cytochrome P-450b and P-450e in the inductive phase of phenobarbital administration.