The Evolution Of The CYP2D Subfamily Gene In Primates

Cytochrome P450(CYP)enzyme is a superfamily of heme proteins that catalyze the oxidation of exogenous and endogenous substances.CYPs have been well studied in mammals,especially in humans(Homo sapiens).It has been found that 12 functional CYP genes in CYPs are closely related to the metabolism of 70?80% of commonly used drugs.CYP2D6 is one of the functional genes,and it is a member of the CYP2 D subfamily of genes.Current studies on the CYP2 D subfamily gene have focused on primates.Primates are an order in class Mammalia,found chiefly in Asia,Africa and the warm regions of America.The habitat of primates is restricted by many factors such as their own characteristics,habitat,foraging difficulty and predation risk,among which foraging difficulty is the more important factor.The difficulty of foraging has a great influence on the habitat selection of animals.Different habitats have different food resources,which leads to the differences in the food composition of primates,and thus the differences in their feeding preferences.In the process of evolution,plants can make chemical defense by producing secondary metabolites with certain odor or toxicity in order to avoid being eaten by animals.However,under survival pressure,animals will take corresponding measures according to the defense mechanism of plants.For example,the human CYP2D6 enzyme can detoxify alkaloids.The CYP2 D gene was amplified in five primate species in this study,which were Trachypithecus leucocephalus,Trachypithecus francoisi,Pygathrix nemaeus,Macaca mulatta,and Macaca assamensis.At the same time,the CYP2 D gene of 35 primates(include Trachypithecus francoisi,Pygathrix nemaeus and Macaca mulatta)was obtained by bioinformatics method.Bioinformatics software such as Editplus3,Clustalx,Paml 4.7,Mega6.0 and Bio Edit were used to analyze the base composition,sequence length,homology,phylogeny and selective pressure of the obtained CYP2 D subfamily gene.The results were as follows:(1)The total number of CYP2 D genes in five primates was the same,but the number of complete genes and pseudogenes were not.The sequence length of the complete gene is relatively stable,which is 1494 bp.(2)Combining the CYP2 D genes obtained by the experiment and the CYP2 D genes obtained by searching,a total of 84 CYP2 D genes were obtained from 37 primates,including 41 complete genes,14 partial genes and 29 pseudogenes.(3)On the whole,there was no significant difference in the proportion of base composition of the same gene in different species,nor in the proportion of base composition of different genes in the same species.In sum,the base(adenine(A),guanine(G),cytosine(C),and thymine(T))composition of intact CYP2 D subfamily genes is that the content of C is the most,the content of A is the least,and the content of C+G is far greater than the content of A+T.(4)Homologous comparison showed that the highest nucleotide similarity of CYP2D6 and CYP2D8 genes in primates was found in Trachypithecus leucocephalus and Trachypithecus francoisi(the CYP2D6 similarity of Trachypithecus leucocephalus and Trachypithecus francoisi was 99.53%,while their CYP2D8 similarity was 100%).The highest amino acid similarity of the CYP2D8 gene was found in Trachypithecus leucocephalus and Trachypithecus francoisi(100%).The highest amino acid similarity of the CYP2D6 gene was found in Theropithecus gelada and the Papio anubis(99.60%).(5)The gene trees constructed by CYP2D6,CYP2D8 and all the intact CYP2 D subfamily genes were basically the same as the species tree,but there were differences among species within the genus.(6)Phylogenetic independent contrast analysis was used to analyze the total gene number and complete gene number of CYP2 D and feeding preferences in primates.It was found that the total gene number and complete gene number of CYP2 D were negatively correlated with feeding preferences,but P value was not significant(ρ=-0.03,p=0.85;ρ=-0.22,p= 0.19).It was found that feeding preferences were not related to the total gene number or the complete gene number of CYP2 D.(7)There is no significant difference in the average number of CYP2 D genes in primates with different diets(p=0.21),while the total number of CYP2 D genes in primates with different diets is significantly different(p=0.00),which means that in primates the difference in the total number of CYP2 D genes in carnivorous animals,omnivorous animals and herbivorous animals was statistically significant.(8)On the whole,CYP2D6,CYP2D8,and all intact CYP2 D subfamily genes were under purifying selection.In the site model,CYP2D6 and all complete CYP2 D subfamily genes selected alternative hypotheses and rejected the null hypothesis,that is,M2 a and M8 models are better than M1 a,M7 and M8 a models.In addition,CYP2D6 and all complete CYP2 D genes have positive selection sites in M2 a and M8 models.In CYP2D8,the M8 model is better than the M7 and M8 a models,and there are positive selection sites,but there are no positive selection sites in M2 a.(9)On the whole,the CYP2 D subfamily gene of herbivores,carnivores and omnivores were under purifying selection,which were significantly different from those in the M0(ω=1)model(p= 6.40E-83,1.15E-71 and 3.81E-41,respectively).In the site model,the CYP2 D subfamily gene of herbivores and omnivores had positive selection sites in M2 a and M8 models,and the positive selection sites in the M8 model were more than those in M2 a.The complete CYP2 D subfamily gene of carnivorous animals had no positive selection sites in either the M2 a or M8 models.(10)Exons of CYP2D6,CYP2D8,and all intact CYP2 D subfamily genes(including CYP2D6,CYP2D8,and other intact CYP2 D subfamily genes)were under purifying selection,which were significantly different from those of the M0(ω=1)model(except for exon5 of CYP2D8).