乌苏里貉MC3R基因密码子偏好性分析

doi:10.16431/j.cnki.1671-7236.2024.04.003

摘要/Abstract

摘要： 【目的】明确乌苏里貉黑素皮质素受体3(melanocortin 3 receptor,MC3R)基因密码子使用偏好特征和影响因素,了解不同物种间遗传进化和密码子偏好性的关系,为开展MC3R基因异源高效表达研究提供理论依据。【方法】以乌苏里貉和其他15个物种的MC3R基因CDS序列为材料,应用Codon W、EMBOSS等软件分析MC3R基因密码子偏好性的6个参数指标;通过Neutrality-plot、ENc-plot及PR2-plot分析探究密码子偏好性形成的影响因素;基于各物种MC3R基因CDS序列信息构建系统发育树,基于同义密码子相对使用度(RSCU)构建不同物种的密码子使用偏好性热图。【结果】乌苏里貉MC3R基因密码子GC和GC3s均＞0.5,密码子偏好使用以G/C结尾;偏好使用的密码子有25个(RSCU值＞1),其中16个以C结尾,9个以G结尾。经Neutrality-plot、ENc-plot及PR2-plot分析得出,自然选择是MC3R基因密码子使用偏好形成的主要影响因素。基于基因序列和RSCU值的聚类分析显示,在系统进化上乌苏里貉与犬属同一分支,后与赤狐、北极狐聚为一支;但在密码子使用上乌苏里貉与人、黑猩猩及家马聚为一类。【结论】MC3R基因偏好使用以G/C结尾的密码子;自然选择是导致偏好性产生的主要影响因素;密码子使用虽具有种属特异性,但受其他因素影响亲缘关系相近的物种间密码子使用模式也会有差异。

关键词: 乌苏里貉; MC3R基因; 密码子偏好性; 自然选择

Abstract: 【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.

Key words: Nyctereutes procyonoides; MC3R gene; codon usage bias; natural selection

中图分类号:

李鑫, 李伟, 刘洁, 程静然, 刘进军, 王朋然, 韩学良, 任二军, 邓露芳, 宗文丽. 乌苏里貉MC3R基因密码子偏好性分析[J]. 中国畜牧兽医, 2024, 51(4): 1349-1361.

LI Xin, LI Wei, LIU Jie, CHENG Jingran, LIU Jinjun, WANG Pengran, HAN Xueliang, REN Erjun, DENG Lufang, ZONG Wenli. Analysis of Codon Usage Bias of MC3R Gene in Nyctereutes procyonoides[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(4): 1349-1361.

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