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基于裸大麦、普通大麦和野生大麦叶绿体基因组编码序列，分析其密码子使用偏好及差异.结果显示，3者不同窗口大小的胞嘧啶和鸟嘌呤（GC）含量在密码子不同位点（GC1、GC2、GC3）呈梯度递减趋势（46.74%/46.80%/46.63%、39.47%/39.43%/39.43%、29.80%/29.75%/30.25%），且均存在31个高偏好密码子（RSCU>1），其中29个以A/U结尾，呈现显著NNA/NNU结尾偏好.叶绿体基因组有效密码子数（ENC）值（47.14、47.02、47.75）及ENC>45的基因占比（39、39、42个）表明整体密码子偏好性较弱.中性绘图、ENC-plot和PR2-plot分析证实自然选择是密码子偏好形成的主要驱动力.栽培大麦（裸大麦与普通大麦）在GC组成、ENC分布及最优密码子（含特有GCA/AGA）上高度趋同，提示人工驯化通过纯化选择强化了有益性状的遗传稳定性，为解析大麦驯化分子机制提供了新视角.
Abstract：The codon usage preferences and differences among cultivated and wild barley, Hordeum vulgare var.Coleste, H. vulgare ssp. vulgare and H. vulgare ssp. spontaneum, were analyzed based on the coding sequences of their chloroplast genomes. The results demonstrated that the cytosine and guanine(GC) content at different codon positions(GC1, GC2, GC3) exhibited a gradient decrease across the three species(46. 74%/46. 80%/46. 63%, 39. 47%/39. 43%/39. 43%, 29. 80%/29. 75%/30. 25%). All three species shared 31 highly preferred codons(RSCU > 1), with 29 of these codons ending in A/U, indicating a significant preference for NNA/NNU endings.The effective codon number(ENC) values of the chloroplast genomes(47. 14, 47. 02, 47. 75) and the proportion of genes with ENC > 45(39, 39, 42) suggested a relatively weak overall codon preference. Neutral plotting, ENC-plot, and PR2-plot analyses confirmed that natural selection was the primary driving force behind the formation of codon preferences. Furthermore, two cultivated barley exhibited high convergence in terms of GC composition, ENC distribution, and optimal codons(including specific GCA/AGA). This suggests that artificial selection through purifying selection has enhanced the genetic stability of beneficial traits, offering new insights into the molecular mechanisms underlying barley domestication.
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基本信息:
DOI：
中图分类号:S512.3
引用信息:
[1]谢刘义,任璇,应文博等.栽培大麦和野生大麦叶绿体基因组密码子偏好性比较分析[J].云南民族大学学报(自然科学版),2025,34(03):268-276.
基金信息:
云南省高层次人才培养支持计划项目（YNWR-QNBJ-2020-287）; 国家中医药管理局全国中药资源普查项目（GZY-KJS-2018-004）