Analysis of Codon Usage Bias of MC3R Gene in Nyctereutes procyonoides
[Objective]This study was aimed to identify the codon usage characteristic and influencing factors of melanocortin 3 receptor(MC3R)gene in Nyctereutes procyonoides,and understand the relationship between genetic evolution and codon preference among different species,so as to provide a theoretical basis for studying the heterologous high expression of MC3R gene.[Method]Six parameters of codon preference of MC3R gene CDS sequences in Nyctereutes procyonoides and 15 other species were analyzed using Codon W and EMBOSS softwares,and Neutrality-plot,ENc-plot and PR2-plot were used to explore influence factors of codon bias formation of MC3R gene.The phylogenetic tree was constructed based on the cluster analysis of MC3R gene CDS sequence information,and the heat map was constructed base on relative synonymous codon usage(RSCU)of different species.[Result]The codon GC and GC3s were both greater than 0.5 of MC3R gene in Nyctereutes procyonoides,and the codon preferred to end with G/C.There were 25 preferred codons(RSCU value＞1),of which 16 ended in C and 9 ended in G.Neutrality-plot,ENc-plot and PR2-plot analysis results showed that natural selection was the main influencing factor of MC3R gene codon preference formation.The cluster analysis results of gene sequence and RSCU values showed that the Nyctereutes procyonoides belonged to the same cladistic genus as Canis lupus familiaris in phylogenetic relationship,and then clustered with Vulpes vulpes and Vulpes lagopus.But when it came to codon use,Nyctereutes procyonoides were grouped with Homo sapiens,Pan troglodytes and Equus caballus.[Conclusion]MC3R gene prefered to use codons ending with G/C,and natural selection was the main influencing factor of codon preference.The codon usage bias was species-specific,but codon use patterns were different among closely related species due to other factors.
万方数据
维普
