仙人掌科叶绿体与核基因组密码子偏好性分析  

Codon Preference Analysis of the Chloroplast and Nuclear Genomes in Cactaceae

作　　者：林新茂 黄家权[1] Lin Xinmao;Huang Jiaquan(College of Tropical Crops,Hainan University,Haikou,570100)

机构地区：[1]海南大学热带作物学院,海口570100

出　　处：《分子植物育种》2024年第22期7400-7412,共13页Molecular Plant Breeding

基　　金：农业农村部物种品种资源保护(热带作物)项目(18190033-1)资助。

摘　　要：为了研究仙人掌科植物叶绿体基因组密码子使用模式,选择16种仙人掌科植物的叶绿体基因组进行密码子偏好性分析,并且分析量天尺(Selenicereus undatus)的核基因组密码子偏好性,比较其与叶绿体基因组的异同。使用CodonW 1.4.2和EMBOSS在线软件对仙人掌科叶绿体基因组序列进行密码子分析,获得有效密码子数、密码子GC含量和相对同义密码子使用度等参数,然后进行中性绘图分析、ENc-plot分析和PR2-plot分析,进而获得最优密码子。结果表明,16种仙人掌科植物的平均有效密码子数为50.04,整体密码子偏好性较弱。GC_3与GC_(12)回归系数在0.22~0.68之间,平均为0.39,密码子使用偏好性受自然选择因素的影响大于碱基突变因素,且不同物种间变化较大。ENc-plot结果显示一部分基因的ENc值与预期值较近,一部分基因落于预测曲线下方,表明密码子偏好性受碱基突变和自然选择等多种因素共同影响。PR2-plot分析发现所有物种叶绿体密码子第三位存在明显的T/G偏倚。半胱氨酸的UGU (TGT)密码子被16种仙人掌科植物共同作为最优密码子。S. undatus的核基因组与叶绿体基因组的密码子偏好性存在显著差异,在核基因组中,密码子偏好性主要受自然选择等因素影响,几乎不受碱基突变影响,并且密码子使用更加多样化。To study the codon usage patterns of the chloroplast genome in Cactaceae, 16 chloroplast genomes of Cactaceae were selected for codon preference analysis. The codon preference of the nuclear genome of Selenicereus undatus was analysied and compared with that of the chloroplast genome to identify similarities and differences.Codon analysis of the chloroplast genome sequence of Cactaceae was performed using CodonW 1.4.2 and EMBOSS online software to obtain parameters such as effective number of codons(ENc), codon GC content and relative synonymous codons usage(RSCU). Neutral plotting, ENc-plot, and PR2-plot analyses were then conducted to identify the optimal codons. The results showed that the average ENc of 16 species in Cactaceae was 50.04 and the overall codon preference was weak. The regression coefficients of GC3and GC12ranged from 0.22 to 0.68, with an average of 0.39. The codon usage preference was more influenced by natural selection factors than base mutation factors,and was more variable among species. The ENc-plot results showed that the ENc values of some genes were close to the expected values, and some genes fell below the predicted curve, indicating that codon preference is influenced by a combination of factors such as base mutations and natural selection. PR2-plot analysis revealed a significant T/G bias in the third position of the chloroplast codon in all species. The UGU(TGT) codon for cysteine is shared as the optimal codon by 16 species of Cactaceae. The codon preferences of the nuclear and chloroplast genomes of S. undatus are significantly different. In the nuclear genome, codon preferences are mainly influenced by factors such as natural selection and are less affected by base mutations, resulting in more diverse codon usage.

关 键 词：仙人掌科 密码子使用特征 叶绿体基因组 最优密码子 

分 类 号：Q943.2[生物学—植物学]