思茅松及云南松转录组密码子偏好性比较分析  

Comparison between the codon preferences of the transcriptomes of Pinus kesiya and Pinus yunnanensis

作　　者：原晓龙 王毅 罗婷 李云琴 毕玮 陈伟 李江 YUAN Xiaolong;WANG Yi;LUO Ting;LI Yunqin;BI Wei;CHEN Wei;LI Jiang(Yunnan Provincial Key Laboratory of Cultivation and Exploitation of Forest Plants,Kunming 650201,Yunnan,China;Key Laboratory of the National Forestry and Grassland Administration for Conservation of Rare,Endangered&Endemic Forest Plants,Yunnan Academy of Forestry and Grassland,Kunming 650201,Yunnan,China)

机构地区：[1]云南省林业和草原科学院,云南省森林植物培育与开发利用重点实验室,云南昆明650201 [2]云南省林业和草原科学院,国家林业和草原局云南珍稀濒特森林植物保护和繁育重点实验室,云南昆明650201

出　　处：《中南林业科技大学学报》2023年第9期153-163,共11页Journal of Central South University of Forestry & Technology

基　　金：云南省重点研发计划项目(202102AE090022);云南省种子种业联合实验室工业思茅松品种选育项目(202202AR070001-17);云南省森林植物培育与开发利用重点实验室开放基金项目(KFJJ21-03);云南省中青年学术和技术带头人后备人才项目(202205AC160044)。

摘　　要：【目的】比较思茅松Pinus kesiya var.langbianensis和云南松P.yunnanensis转录组中表达基因的密码子使用模式,为运用基因工程技术改造密码子实现思茅松基因异源表达提供理论依据。【方法】利用CodonW1.4.2软件分析思茅松不同组织和云南松转录组密码子碱基组成,同时统计和计算其他相关参数,推断其最优密码子并将其与其他物种的密码子使用频率进行比较。【结果】在云南松和思茅松根转录组密码子的碱基组成方面,云南松为GC12(0.50)>GC3s(0.47),思茅松根为GC12(0.51)>GC3s(0.32);在思茅松不同组织转录组的碱基组成方面,高产脂树皮为GC12(0.49)>GC3s(0.45),低产脂树皮为GC12(0.50)>GC3s(0.41),说明云南松和思茅松不同组织转录组的密码子在第3位上均偏好以AU结尾;它们的CAI值相较于被子植物均较低,这些均说明云南松和思茅松不同组织转录组密码子的偏好性均较弱;且其中性绘图分析和ENC-plot分析说明它们的使用模式均主要受到选择压力的影响;最优密码子分析显示云南松和思茅松根的最优密码子差异较小。通过对思茅松、拟南芥、构巢曲霉、酵母、毛果杨和云南松的密码子使用频率进行比较,发现思茅松与云南松转录组的密码子偏好性极为相似,与构巢曲霉和拟南芥的相对接近,说明构巢曲霉真核表达系统更适合思茅松基因的异源表达。【结论】思茅松和云南松转录组编码序列的密码子使用偏性以选择影响为主,是多种因素共同作用的结果,构巢曲霉是思茅松基因异源表达的最佳表达受体。该结论为今后开展思茅松转基因育种、特定基因的异源表达和生物合成中提高外源基因表达效率提供理论基础和参考依据。【Objective】The comparison of the codon usage patterns in the transcriptomes of Pinus kesiya and P.yunnanensis provided a basis for the codon modification of hetero-expression of P.kesiya genes.【Methods】In the present study,the codon base composition and other relative parameters of the transcriptomes of P.kesiya and P.yunnanensis were analyzed and calculated using Codon W 1.4.2,and the optimal codon was deduced and compared with the codon usage frequency of other fungus and plants.【Results】The base composition of the transcriptome of P.yunnanensis was GC12(0.50)>GC3s(0.47),and the composition of the P.kesiya transcriptome was GC12(0.51)>GC3s(0.32).In terms of the base composition of the transcriptomes of different tissues,the high-resin bark was in the order of GC12(0.49)>GC3s(0.45),and the low-resin bark was in the order of GC12(0.50)>GC3s(0.41),which illustrated that their codons all preferred AU at the third base of the transcriptome of different tissues of P.yunnanensis and P.kesiya.All their CAI values were relatively lower than those of angiosperms,indicating the transcriptome codon preference of different tissues of P.yunnanensis and P.kesiy.The neutrality plot and ENC-plot analysis indicated that their usage patterns were mainly affected by selection pressures.The optimal codons had a small difference between the transcriptome of different tissues of P.kesiya and P.yunnanensis.The codon usage frequency of P.kesiya,P.yunnanensis,Arabidopsis thaliana,Populus trichocarpa,Aspergillus nidulans and Saccharomyces prombe was compared,and the results revealed that the codon preferences of P.kesiya and P.yunnanensis were pretty similar,which were relatively close to those of A.niger and A.thaliana,illustrating that the eukaryotic expression system of A.nidulans was more suitable for the heterologous expression of the P.kesiya genes.【Conclusion】The codon usage bias of the transcriptome coding sequences of P.yunnanensis and P.kesiya was mainly affected by selection and the joint action of many factors

关 键 词：思茅松 云南松 转录组 密码子使用模式 密码子偏好性 密码子使用频率 

分 类 号：S718.46[农业科学—林学]