Codon usage bias analysis of rbcL genes of 20 Lythraceae species
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摘要:
目的 分析千屈菜科Lythraceae植物rbcL基因密码子使用特性，明确密码子偏好性的影响因素，筛选rbcL基因异源表达和遗传转化的合适受体。 方法 从美国国家生物技术信息中心(NCBI)获取20种千屈菜科植物的rbcL基因全长编码区序列(CDS)数据，运用CodonW、EMBOSS和DAMBE软件获取基因碱基组成和密码子使用偏好性的相关参数，分析该类植物叶绿体rbcL基因使用密码子的偏倚性及其影响因素。 结果 千屈菜科植物rbcL基因GC含量(GC)为0.425~0.437，密码子第3位碱基GC含量(GC3s)为0.275~0.300。GC3s、GC与有效密码子数(ENC)相关显著(P＜0.01)；ENC-GC3s散点图分析、中性绘图分析、奇偶偏差分析均表明：相较于突变压力，自然选择压力对千屈菜科植物rbcL基因密码子使用偏好性的影响更大。基于同义密码子相对使用度的系统聚类与CDS邻接树结果部分一致。与千屈菜科rbcL基因密码子平均使用频率相比，大肠杆菌Escherichia coli、酵母Saccharomyces cerevisiae、拟南芥Arabidopsis thaliana、烟草Nicotiana tabacum和番茄Solanum lycopersicum分别存在28、26、20、19和17个使用频率相差较大的密码子。 结论 千屈菜科植物rbcL基因碱基组成上更倾向于选择A/T碱基，且偏好使用末端A/T碱基的密码子；rbcL基因密码子使用偏好性受多种因素共同作用，但自然选择压力是最主要因素；密码子偏好性的系统聚类可为系统发育研究提供补充；酵母更适合作为千屈菜科植物rbcL基因异源表达受体，番茄更适合作为rbcL基因遗传转化和功能研究的受体材料。图6表3参32 Abstract:Objective With an analysis of the codon usage characteristics of the rbcL genes in Lythraceae species, this study is aimed to clarify the influencing factors of codon bias, and screen the optimal receptor for heterologous expression and genetic transformation. Method After rbcL gene CDS of 20 Lythraceae species were obtained from NCBI, CodonW, EMBOSS, and DAMBE software were utilized to compute relevant parameters of gene base composition and codon usage bias before an analysis is conducted of the usage bias of such genes and its incluencing factors using SPSS and Origin software. Result The GC content of the rbcL gene from Lythraceae species ranged from 0.425 to 0.437, with GC3s being 0.275 to 0.300 and there was a significant correlation between GC3s, GC, and ENC(P＜0.01). As was shown in the analysis of ENC-GC3s plot, the neutral plot and PR2, natural selection pressure affected the codon usage bias of the rbcL gene from Lythraceae species more heavily than mutation pressure. The result of clustering analysis based on RSCU is partially consistent with that of the neighbor-joining tree based on CDS. Compared with the average codon usage frequency of the rbcL gene from the 20 Lythraceae species, Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, Nicotiana tabacum, and Solanum lycopersicum possessed 28, 26, 20, 19 and 17 codons, respectively, with significant differences in usage frequency. Conclusion In terms of the base composition of the rbcL gene from 20 Lythraceae species, there was a tendency towards A/T bases and codons with A/T base at ther termonal were generally preferred. Also, of all the factors having an influence on codon bias, natural selection pressure was the most important one. Systematic clustering is a good complement for phylogenetic analysis. S. cerevisiae is more suitable as a heterologous expression receptor, while S. lycopersicum is more suitable to act as a receptor material for genetic transformation and function research of rbcL gene. [Ch, 6 fig. 3 tab. 32 ref.] -
Key words:
- base composition /
- selection pressure /
- mutation pressure /
- clustering analysis /
- receptor
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图 5 基于rbcL基因CDS的邻接树(左)和基于59个密码子RSCU的聚类树状图(右)
Figure 5 NJ tree based on CDS of rbcL genes (left) and cluster dendrogram based on RSCU of 59 codons (right)
图 6 千屈菜科植物与模式生物密码子使用频率比值
Figure 6 Ratios of codon usage frequency of Lythraceae species to model organisms
表 1 20种千屈菜科植物rbcL基因信息
Table 1. Information of rbcL genes from 20 Lythraceae species
物种 GenBank登录号 CDS位置 物种 GenBank登录号 CDS位置 萼距花 Cuphea hyssopifolia MN833211 58955~60382 南洋紫薇 Lagerstroemia siamica MK881628 55129~56556 八宝树 Duabanga grandiflora MK881638 56823~58250 绒毛紫薇 Lagerstroemia tomentosa MK881632 54873~56300 黄薇 Heimia myrtifolia MG921615 58612~60039 西双紫薇 Lagerstroemia venusta MK881630 55159~56586 副萼紫薇 Lagerstroemia calyculata MK881636 54873~56300 散沫花 Lawsonia inermis MK881631 58836~60263 川黔紫薇 Lagerstroemia excelsa MK881635 54910~56337 千屈菜 Lythrum salicaria MK881629 59099~60526 屋久岛紫薇 Lagerstroemia fauriei NC_029808 54810~56237 石榴 Punica granatum NC_035240 59017~60444 多花紫薇 Lagerstroemia floribunda NC_031825 54776~56203 圆叶节节菜 Rotala rotundifolia MK881626 58835~60262 桂林紫薇 Lagerstroemia guilinensis NC_029885 54697~56124 细果野菱 Trapa maximowiczii NC_037023 58322~59770 云南紫薇 Lagerstroemia intermedia NC_034662 54948~56375 欧菱 Trapa natans MK881634 58387~59814 福建紫薇 Lagerstroemia limii MK881627 54830~56257 虾子花 Woodfordia fruticosa MK881637 59444~60871 
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表 2 20种千屈菜科植物rbcL基因碱基组成和密码子使用特性
Table 2. Base composition and codon usage characteristics of rbcL genes from 20 Lythraceae species
物种 A3s T3s G3s C3s GC GC1s GC2s GC3s CAI ENC 萼距花 0.376 0.531 0.157 0.173 0.435 0.582 0.437 0.286 0.276 45.392 八宝树 0.380 0.526 0.152 0.180 0.431 0.571 0.433 0.288 0.278 45.942 黄薇 0.390 0.508 0.145 0.194 0.434 0.571 0.433 0.296 0.283 46.540 副萼紫薇 0.377 0.525 0.148 0.186 0.432 0.576 0.429 0.292 0.277 45.635 川黔紫薇 0.376 0.526 0.149 0.187 0.432 0.571 0.431 0.294 0.275 45.743 屋久岛紫薇 0.379 0.529 0.146 0.184 0.431 0.571 0.431 0.290 0.272 45.659 多花紫薇 0.378 0.526 0.148 0.184 0.432 0.576 0.429 0.292 0.276 45.625 桂林紫薇 0.376 0.526 0.149 0.187 0.432 0.571 0.431 0.294 0.275 45.743 云南紫薇 0.379 0.526 0.140 0.191 0.431 0.571 0.431 0.290 0.275 45.340 福建紫薇 0.379 0.531 0.142 0.184 0.430 0.571 0.431 0.288 0.274 45.564 南洋紫薇 0.379 0.526 0.140 0.191 0.431 0.571 0.431 0.290 0.275 45.340 绒毛紫薇 0.377 0.525 0.148 0.186 0.432 0.576 0.429 0.292 0.277 45.635 西双紫薇 0.379 0.526 0.140 0.191 0.431 0.571 0.431 0.290 0.275 45.340 散沫花 0.379 0.536 0.151 0.171 0.429 0.569 0.435 0.282 0.276 45.264 千屈菜 0.389 0.535 0.138 0.173 0.428 0.576 0.433 0.275 0.285 45.007 石榴 0.381 0.518 0.153 0.184 0.436 0.578 0.437 0.294 0.275 46.153 圆叶节节菜 0.379 0.536 0.151 0.171 0.429 0.569 0.435 0.282 0.276 45.264 细果野菱 0.387 0.532 0.154 0.165 0.425 0.567 0.431 0.277 0.274 44.181 欧菱 0.387 0.532 0.154 0.165 0.426 0.569 0.431 0.277 0.274 44.029 虾子花 0.376 0.516 0.163 0.184 0.437 0.576 0.435 0.300 0.270 46.458
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表 3 碱基组成与密码子使用偏好相关性
Table 3. Correlation between base composition and codon usage bias
参数 CAI ENC GC GC1s GC2s GC3s ENC 0.062 GC − 0.136 0.855** GC1s 0.138 0.403 0.712** GC2s 0.029 0.229 0.348 0.314 GC3s − 0.264 0.856** 0.846** 0.324 − 0.074 GC12 0.112 0.403 0.684** 0.869** 0.743** 0.190 说明：**表示在0.01水平上显著相关(双尾)
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