摘要
[目的]为解析甘蔗基因组的密码子使用特征,提高异源基因在甘蔗中的表达效率.[方法]以已发布的甘蔗属种(热带种LA-purple、割手密NP-X和AP85-441)及其近缘属种蔗茅(Yunnan2009-3)基因组为数据,利用Python、CodonW1.4.2 进行密码子偏好性分析,同时通过中性绘图、ENC-plot、PR2-plot等分析探讨密码子偏好性形成的影响因素,并结合转录组测序数据分析密码子偏好性参数与基因表达水平的相关性.最后,基于RSCU均值与 7 个主要模式生物种(玉米、高粱、水稻、拟南芥、烟草、大肠杆菌、酿酒酵母)的密码子使用模式进行比较分析.[结果]显示热带种、割手密和蔗茅的基因组都富含GC,平均GC含量为 56.3%,且GC3>GC1>GC2,倾向于使用以G/C结尾的密码子,平均ENC值为 48.45,偏好性较低.中性绘图、ENC-plot和PR2-plot分析表明它们的密码子偏好性受到自然选择、突变压力等多种因素的共同影响,其中自然选择占主导作用.相关性分析表明密码子偏好性参数与基因实际的转录表达水平存在显著相关性,但相关性不强.根据RSCU和∆RSCU值,确定了 13 个最优密码子,均以C或G结尾,密码子使用特性在全基因组和染色体组水平上无差异.通过比较发现,甘蔗的核苷酸组成及密码子偏好性与玉米、高粱和水稻较为相似,而与拟南芥、烟草、大肠杆菌和酵母具有显著差异.[结论]甘蔗热带种、割手密和蔗茅的密码子偏好性高度相似,其形成受自然选择和突变因素的影响.此外,对甘蔗优异基因功能异源验证时可优先选择玉米、水稻和高粱作为异源表达系统.
Abstract
[Objective]To clarify the codon usage characteristics and improve expression efficiency of exogenous genes in sugarcane.[Method]Codon usage bias were analyzed by Python and CodonW1.4.2 tools based on their genomes data of three species including Saccharum officinarum(LA-purple),S.sponaneum(NP-X and AP85-441),and Erianthus fulvus(Yunnan2009-3).Neutrality-plot,ENC-plot,and Parity Rule 2(PR2)-plot analysis were also used to explore the possible factors that affect the formation of codon usage bias.Simultaneously,correlation analysis between gene expressions and codon usage bias parameters was carryd out based on transcriptome data.Finally,a comparison analysis of codon usage patterns were performed between sugarcane and the other seven main model organisms,namely,Zea mays,Sorghum bicolor,Oryza sativa,Arabidopsis thaliana,Nicotiana tabacum,Escherichia coli,and Saccharomyces cerevisiae based on the average RSCU value of three species.[Result]S.officinarum,S.sponaneum,and E.fulvus were rich in GC base pairs,the average GC content was 56.3%,and GC3 was the highest,followed by GC1 and GC2,indicating that sugarcane preferred to use synonymous codons ending with a C/G base.The average ENC value was 48.45,suggesting that sugarcane had a lower codon usage bias.According to the results of neutral-plot,ENC-plot,and PR2-plot analysis,the codon usage bias of four genomes was affected by natural selection,mutation pressure,and so on,and the natural selection dominated in them.Correlation analysis showed that codon preference parameters were significantly correlated with the actual transcription expressions of genes,but the correlation was not strong.Based on the RSCU and ∆RSCU values,thirteen identical optimal codons were confirmed,and all of them were ended with C/G base pairs.The codon usage characteristics were not different at genome-wide and chromosome level.In addition,the codon usage bias of sugarcane was similar to that of Z.mays,S.bicolor,and O.sativa,while it had a significant difference with A.thaliana,N.tabacum,E.coli,and S.cerevisiae.[Conclusion]The codon usage bias among S.officinarum,S.sponaneum and E.fulvus was highly similar,and its formation was affected by natural selection and mutation pressure factors.Meanwhile,Z.mays,O.sativa and S.bicolor could be used for elite gene function research on sugarcane as a exogenous expression system on account of their codon usage bias patterns.
基金项目
云南种子种业联合实验室项目(202205AR070001-09)
云南省科技人才与平台计划(202205AM070001)
国家科技期刊平台
NSTL
万方数据