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    杜鹃花属植物叶绿体基因组系统发育与密码子使用偏好性分析

    Phylogenetic Analysis and Codon Usage Bias of Chloroplast Genomes in Rhododendron

      摘要
    • 摘要:
      目的 解析杜鹃花属（Rhododendron）植物叶绿体基因组密码子使用模式，为杜鹃花属种质资源保护和创新提供遗传信息，为其遗传改良与系统发育研究奠定基础。
      方法 以46种杜鹃花属植物叶绿体基因组为研究对象，利用mafft及iQtree软件研究杜鹃花属物种系统发育。利用Codon W 1.4.2、R语言及EMBOSS等软件，对叶绿体基因组的密码子GC含量、同义密码子相对使用度（RSCU）、有效密码子数（ENC）等参数进行分析。通过中性绘图、PR2-plot及最优密码子分析，探究杜鹃花属植物密码子使用偏好特征及主要影响因素。
      结果 46种杜鹃花属植物系统发育树显示杜鹃花属包含3个主要分支，第1支包括常绿杜鹃亚属（Hymenanthes）和羊踯躅亚属（Pentanthera）；第2支主要有杜鹃亚属（Rhododendron），包括迎红杜鹃（R. mucronulatum）；而第3支包括映山红亚属（Tsutsusi）和马银花亚属（Azaleastrum）。杜鹃花属植物叶绿体基因组密码子的GC含量在GC1、GC2、GC3和GCall上相对接近，且均呈现GC1 > GC2 > GC3的规律，其中GC3含量的变化范围小于GC1和GC2，表明GC含量在不同密码子位置的分布不均匀。杜鹃花属植物叶绿体基因组密码子的RSCU值为0.3123~2.156。杜鹃花属植物叶绿体基因组密码子的ENC值主要为35~55，说明其密码子使用偏好性较弱。杜鹃花属植物的叶绿体基因组密码子倾向于以A/U结尾，使用偏好性同时受突变压力和自然选择的影响，且受自然选择影响更大。马银花亚属叶绿体基因组密码子使用偏好性受自然选择影响大于其他亚属。杜鹃花属植物的叶绿体基因组共鉴定出7个最优密码子，其中以A/U结尾居多，主要编码不带电荷的氨基酸。
      结论 杜鹃花属植物叶绿体基因组密码子的使用偏好主要受自然选择影响。

       

      Abstract:
      Objective The objective of this study was to analyze the codon usage patterns in the chloroplast genome of Rhododendron, aiming to provide genetic information for the conservation and innovation of Rhododendron germplasm resources and to lay a foundation for its genetic improvement and phylogenetic research.
      Method The chloroplast genomes of 46 Rhododendron species were taken as the research objects. The phylogenetic relationships of Rhododendron were investigated using mafft and iQtree software. Software such as Codon W 1.4.2, R language, and EMBOSS were utilized to analyze parameters of codons in the chloroplast genome, including GC content, relative synonymous codon usage (RSCU), and effective number of codons (ENC). Additionally, neutrality plot, PR2-plot, and optimal codon analysis were carried out to explore the characteristics of codon usage preference and the main influencing factors in Rhododendron plants.
      Result The phylogenetic tree of the 46 Rhododendron species revealed three major clades. Clade I comprised subgenera Hymenanthes and Pentanthera; Clade II mainly consisted of subgenus Rhododendron, including R. mucronulatum; and Clade III included subgenera Tsutsusi and Azaleastrum. The GC1, GC2, GC3, and GCall contents of Rhododendron plants were relatively close, and all species showed a consistent pattern of GC1 > GC2 > GC3. The variation range of GC3 content was smaller than that of GC1 and GC2, indicating the uneven distribution of GC content at different codon positions. The RSCU values of chloroplast genomes in Rhododendron ranged from 0.3123 to 2.156. The ENC values of chloroplast genomes in Rhododendron were mainly concentrated in the range of 35 to 55, indicating weak codon usage bias. The chloroplast genome codons of Rhododendron species tended to end with A or U. Codon usage bias was influenced by both mutation and natural selection, with natural selection playing a more important role. The codon usage bias of the chloroplast genome in subgenus Azaleastrum was more strongly influenced by natural selection than in other subgenera. A total of 7 optimal codons were identified in the chloroplast genomes of Rhododendron species, most of which end with A/U and primarily encode uncharged amino acids.
      Conclusion The codon usage bias in the chloroplast genome of Rhododendron plants is mainly influenced by natural selection.

       

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