目的 研究點地梅屬Androsace L.物種葉綠體基因組蛋白編碼基因密碼子的偏好性及其影響因素。方法 測序了點地梅屬1個物種（西藏點地梅）的葉綠體基因組，其他9物種的序列從NCBI下載。根據(jù)序列篩選條件，共得到41條共有序列。用CodonW 1.4.2計算相關(guān)參數(shù)，Python整理數(shù)據(jù)，R做相關(guān)性分析并繪圖。結(jié)果 點地梅屬各物種密碼子第1、2、3位置堿基組成GC含量表現(xiàn)為GC₁＞GC₂＞GC₃，其中第3位GC含量最小。各位點GC含量相關(guān)性為GC₁、GC₂極顯著，而兩者與GC₃相關(guān)性都不顯著，說明3個位置GC含量變化機制不同。3個位置GC含量都小于50%，表明密碼子傾向于使用A/U堿基，尤其是第3位。從10個物種中共鑒定到13～17個最優(yōu)密碼子。所有基因的有效密碼子數(shù)（effective number of codons，ENC）均大于35，說明密碼子使用整體偏性較弱。中性繪圖、ENC-plot及PR2-plot分析顯示，造成密碼子使用偏性的主要因素是自然選擇，但突變壓對大部分基因的密碼子偏性也有重要影響。系統(tǒng)發(fā)育及聚類分析顯示密碼子偏性在物種間是保守的。結(jié)論 點地梅屬葉綠體基因組蛋白編碼基因傾向于使用A/U堿基編碼的密碼子，自然選擇是影響密碼子偏好性的主要因素。研究結(jié)果能為點地梅屬的分子進(jìn)化、系統(tǒng)發(fā)育及葉綠體基因工程提供基礎(chǔ)。

Objective To study the codon preference of chloroplast genome protein encoding genes and influencing factors in Androsac. Methods The chloroplast genome of Androsace mariae was sequenced, and the sequences of the other nine species were downloaded from NCBI. According to the sequence screening conditions, a total of 41 common sequences were obtained. CodonW 1.4.2 was used to calculate the relevant parameters, Python was used to process the data, R was used for correlation analysis and drawing figures. Results The GC content at the first, second and third positions of the codon was GC₁ > GC₂ > GC₃, and the GC content at the third position was the minimum. The correlation of GC content between GC₁ and GC₂ was extremely significant, but not significant for GC₃ between GC₁ or GC₂, indicating that the change mechanism of GC content at the three sites was different. The GC content of all three sites was less than 50%, indicating that the codons tended to use A/U bases, especially the third position. A total of 13—17 optimal codons were identified from 10 species. Effective number of codons (ENC) of all genes were greater than 35, indicating that the overall bias was weak. Neutral-plot, ENC-plot and PR2-plot analysis showed that the main factor causing codon bias was natural selection, but mutation pressure also had an important influence on the codon bias of most genes. Phylogenetic and cluster analysis showed that codon bias was conserved in species. Conclusion The protein coding genes of the chloroplast genome tend to use codons encoded by A/U bases, and natural selection is the main factor affecting codon preference. The results of this study can provide the basis for molecular evolution, phylogeny and chloroplast genetic engineering.

R286.12

青海民族大學(xué)研究生專業(yè)示范思政課程建設(shè)項目（SK-2022-09）