生物学杂志 ›› 2023, Vol. 40 ›› Issue (1): 52-.doi: 10.3969/j.issn.2095-1736.2023.01.052

• 研究报告 • 上一篇    下一篇

高山松叶绿体基因组密码子偏好性模式

李江飞1,2, 李亚麒3, 唐军荣1, 陈 诗1, 陈 林1, 蔡年辉1,2, 许玉兰1,2, 唐红燕4   

  1. 1. 西南林业大学 西南地区生物多样性保育国家林业局重点实验室, 昆明 650224; 2. 西南林业大学 
    西南山地森林资源保育与利用教育部重点实验室, 昆明 650224; 3. 云南省农业科学院热带亚热带
    经济作物研究所, 保山 678000; 4. 普洱市林业和草原科学研究所, 普洱 665099
  • 出版日期:2023-02-18 发布日期:2023-02-21
  • 通讯作者: 许玉兰,博士,教授,博士生导师,主要从事林木遗传育种研究,E-mail: xvyulan@163.com;唐红燕,硕士,正高级工程师,主要从事森林培育研究,E-mail: 519952554@qq.com
  • 作者简介:李江飞,硕士研究生,主要从事林木遗传育种研究,E-mail: 1748056698@qq.com
  • 基金资助:
    国家自然科学基金项目(31860203, 31760204); 云南省万人计划青年拔尖人才项目(09901-80201441); 西南林业大学高值木本油料新种质创制与产业化创新团队项目(2019HC007)

Comparison of codon preference patterns in the chloroplast genome of Pinus densata

LI Jiangfei1,2, LI Yaqi3, TANG Junrong1, CHEN Shi1, CHEN Lin1, CAI Nianhui1,2,XU Yulan1,2, TANG Hongyan4   

  1. 1. Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry
    University, Kunming 650224, China; 2. Key Laboratory for Forest Resources Conservation and Utilization in the
    Southwest Mountains of China Southwest Forestry University, Ministry of Education, Kunming 650224, China;
    3. Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agriculture Sciences, Baoshan 678000, China;
    4. Forestry and Grassland Reaearch Institute of Puer Municipality, Puer 665099, China
  • Online:2023-02-18 Published:2023-02-21

摘要: 为了解高山松叶绿体基因组密码子偏好的使用模式,探讨影响密码子偏好性形成的因素,利用CodonW和CUSP在线软件进行中性绘图分析、ENC-plot、PR2-plot分析和对应性分析。结果显示:高山松叶绿体基因组密码子的平均GC含量为39.84%,GC1、GC2的含量分别为48.81%和40.70%,高于GC3(30.52%),说明其叶绿体基因组密码子末位碱基偏好以A和U结尾;有效密码子数ENC的平均值为48.77,表明其密码子的偏好性较弱;中性绘图分析、ENC-plot分析和PR2-plot偏倚分析表明,选择压力是影响高山松密码子偏好性的主要因素,其次受突变等多种因素的共同影响。进一步对应分析发现,第1轴占总体变异的21.18%,是主要的影响因素,与ENC和GC3无相关关系,但与CAI呈显著相关关系。结果表明:自然选择是影响高山松叶绿体基因组密码子偏好的主要影响因素,也会受到其他因素的影响;有15个密码子被确定为最优密码子,显示出强烈偏向于NNA和NNU密码子的高代表性。研究为今后开展高山松叶绿体基因工程、密码子优化、提高外源基因的表达水平及提高高山松种子的产量和品质提供基础信息。

关键词: 高山松, 叶绿体基因组, 密码子偏好性, 最优密码子

Abstract: To understand the pattern of codon preference used in the chloroplast genome of Pinus densata, the factors that influence the formation of codon preference were explored. Methods such as neutral mapping analysis, ENC-plot, PR2-plot analysis, and correspondence analysis were performed using CodonW and CUSP online software. The results showed that the average GC content of chloroplast codons in P. densata was 39.84%, and the contents of GC1and GC2were 48.81% and 40.70%, respectively, which were higher than GC3(30.52%), indicating that their chloroplast genome codon endings preferred to end with A and U. The mean value of effective codon number ENC was 48.77, indicating a weak codon preference. Results of the neutral plot analysis, ENC-plot analysis, and PR2-plot bias analysis showed that selection pressure was the main factor influencing the codon preference of P. densata, followed by a combination of factors such as mutations. Further correspondence analysis revealed that axis 1 accounted for 21.18% of the overall variation and was the main influencing factor, which was not correlated with ENC and GC3, but was significantly correlated with CAI. The results of these analyses indicated that natural selection was the main influencing factor on chloroplast codon preference in P. densata, and was also influenced by other factors; 15 codons were identified as optimal codons, showing a strong preference for NNA and NNU codons with high representation. This study provided basic information for future genetic engineering of P. densata chloroplasts, codon optimization, improving the expression level of exogenous genes and the yield and quality of alpine pine seeds.

Key words: Pinus densata, chloroplast genome, codon preference, optimal codon

中图分类号: