Journal of Nuclear Agricultural Sciences ›› 2019, Vol. 33 ›› Issue (1): 31-38.DOI: 10.11869/j.issn.100-8551.2019.01.0031

• Induced Mutations for Plant Breeding·Agricultural Biotechnology • Previous Articles     Next Articles

Codon Usage Bias of Canarium album (Lour.) R. Transcriptome and Its Influence Factors

LAI Ruilian, FENG Xin, CHEN Jin, ZHONG Chunshui, CHEN Yiting, WU Rujian*   

  1. Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013
  • Received:2017-07-26 Revised:2017-12-22 Online:2019-01-10 Published:2018-11-20

橄榄转录组密码子使用偏好性及其影响因素

赖瑞联, 冯新, 陈瑾, 钟春水, 陈义挺, 吴如健*   

  1. 福建省农业科学院果树研究所,福建 福州 350013
  • 通讯作者: 吴如健,男,研究员,主要从事果树遗传资源与育种研究。E-mail:wurujian@126.com
  • 作者简介:赖瑞联,男,研究实习员,主要从事果树生物技术与遗传资源研究。E-mail:lairl0618@163.com
  • 基金资助:
    福建省属公益类科研院所基本科研专项(2018R1013-3、2016R1013-15),农业部物种品种资源保护(热带作物)项目(151721301354051701)

Abstract: To explore codon usage bias (CUB) pattern of Canarium album (Lour.) R., the transcriptome of Fulan-1 was used to analyze CUB parameters by codonW and EMBOSS, and the possible formative factors were discussed. The results showed that, the effective number of codon (ENc), GC content (GC) and GC content on the 3rd site (GC3s) is 51.80, 0.435 and 0.377 respectively, which indicate that CUB level of Canarium album (Lour.) R. is low, but it is biased towards the synonymous codons with A or T on the 3 rd site. The differences of relative synonymous codon usage (RSCU) between high-expression and low-expression gene sample groups are not significant, but CGC, ATC, CTC and ACC are defined as the major preference codons of Canarium album (Lour.) R.. Based on composition analysis, neutrality plot, ENc-GC3s plot and PR2 plot, the CUB of Canarium album (Lour.) R. is mainly due to the effect of mutation pressure. In addition, Nicotiana sylvestris and Saccharomyces cerevisiae may be the suitable receptors for gene heterologous transgenosis of Canarium album (Lour.) R.. These results would provide scientific basis for further research of genetic background and molecular evolution of Canarium album (Lour.) R..

Key words: Canarium album(Lour.) R., transcriptome, codon usage bias, mutation

摘要: 为了解橄榄密码子使用偏好特征,以福榄1号橄榄为材料,利用codonW和EMBOSS等软件分析橄榄转录组密码子使用偏好性参数,并探讨偏好性形成的可能因素。结果表明,橄榄转录组平均有效密码子数(ENc)、密码子G和C(GC)含量及密码子第3位上G和C(GC3s)含量分别为51.80、0.435和0.377,表明橄榄转录组密码子使用偏好性较弱,且倾向使用富含A和T且以A或T结尾的密码子。橄榄转录组高低表达基因样本之间同义密码相对使用度(RSCU)差异较小,其中CGC、ATC、CTC和ACC等可作为橄榄最优密码子群。密码子组分分析、中性绘图分析、ENc-GC3s关联分析和偏倚分析结果表明,橄榄转录组密码子使用偏好性可能是以突变压力为主,多种作用方式共同影响的结果。此外,烟草和酵母菌可作为橄榄目标基因异源转化的理想受体系统。本试验结果为进一步研究橄榄遗传背景和分子进化提供了一定的科学依据。

关键词: 橄榄, 转录组, 密码子使用偏好性, 突变