【摘要】 为阐明翅萼石斛（Dendrobium cariniferum）叶绿体基因组密码子使用模式及影响因素，以其52条蛋白编码序列（CDS）为对象，利用EMBOSS在线程序计算各基因及密码子的GC含量，通过CodonW软件计算各基因有效密码子数（ENC）、同义密码子相对使用度（RSCU）、最优密码子使用频率（FOP）及密码子的第3位核苷酸碱基含量等。结果表明：基因组平均GC含量为38%,GC₁>GC₂>GC₃;ENC的值介于37.04～59.52之间，表明密码子使用偏好性较弱；基因组中RSCU>1的密码子有25个，其中11个以U结尾，11个以A结尾，3个以G结尾；中性绘图分析中所有基因均分布于中线对角线上方，GC₁₂与GC₃相关性不显著，密码子使用偏好性以自然选择因素影响为主；ENC-plot绘图分析结果中多数基因分布在标准曲线以下，密码子偏好性主要受自然选择影响；PR2-plot分析表明密码子碱基A和G在密码子第3位比T和C更常见，这表明基因突变会影响密码子使用偏好，但其偏好性可能主要受自然选择影响；共筛选UUU、UUA、AUU等13个以A/U结尾的最优密码子。以上研究结果可为翅萼石斛叶绿体基因组优良基因利用提供理论与基础。更多还原

【Abstract】 This study aims to clarify the codon usage pattern of chloroplast genome in Dendrobium cariniferum Rchb.f.52 protein coding sequences（CDS） were taken as the object.The guanine-cytosine（GC） contents of each gene and codon were calculated by EMBOSS online program.CodonW software was also utilized to calculate the effective codon number（ENC）, relative usage of synonymous codons（RSCU）, optimal codon usage frequency（FOP） and the third nucleotide base content of each gene codon.The results are as follows: the average GC content of the genome was 38%, of which was ranked in the descending order of GC₁>GC₂>GC₃.The value of ENC was between 37.04 and 59.52, indicating the weak preference of codon usage.There were 25 codons with RSCu>1 in the genome, 11 of which were ended with U, while 11 ones were ended with A, and 3 ones were ended with G.All genes were distributed above the diagonal of the midline in neutral mapping analysis.There was no significant correlation between GC₁₂ and GC₃.The codon usage preference was mainly influenced by natural selection factors.Most genes of ENC-plot were distributed below the standard curve.It infers that the natural selection was dominated the codon preference.PR2-plot analysis showed that the codon bases A and G appeared more frequently at codon 3 than T and C.The reason was that the gene mutation was affected codon usage bias, but its preference was mainly affected by natural selection.There were 13 optimal codons in this genome, such as UUU, UUA and AUU, all of which was end in A/U.The finding can provide the theoretical basis for the utilization of excellent genes in chloroplast genome of Dendrobium cariniferum.更多还原