籽粒苋叶绿体基因组密码子偏好性分析

Analysis of Codon Usage in the Chloroplast Genome of Grain Amaranth (Amaranthus hypochondriacus L.)

对筛选出的47条籽粒苋叶绿体基因组蛋白编码序列的密码子使用偏性特征进行分析,结果发现:籽粒苋叶绿体基因组密码子第3位碱基GC的含量较低,为27.31%,即第3位密码子富含A和U;有效密码子数(ENC)值在35.25~61.00之间,基因组中多数蛋白编码序列的密码子使用偏好性偏弱。相对同义密码子使用度(RSCU)分析表明,有29个密码子的RSCU>1,其中密码子第3位碱基以A、U结尾有24个,表明密码子的第3位碱基使用偏好于A和U。中性分析发现,GC3与GC12相关性显著,回归曲线斜率为0.403,表明突变对密码子偏性有极大影响;ENC-plot分析发现,大部分基因落在标准曲线及其附近,表明自然选择也一定程度上影响了密码子偏性。进一步的对应性分析发现,第一轴显示了22.98%的差异,为主要影响因素,其与ENC值的相关性达到显著水平,但与GC3、CBI、GCall相关性不显著。综合分析表明,突变是影响籽粒苋叶绿体基因组密码子偏好性的主要因素,但其他因素也可能有一定影响;UUU、UUA、UCU等24个密码子为最优密码子。

Codon usage bias(CUB)is an important evolutionary feature in a genome,which provides important information for studying organism evolution,gene function,and exogenous gene expression.The CUB and its influencing factors in the chloroplast genome of grain amaranth(Amaranthus hypochondriacus L.)were preliminarily analyzed in this study based on 47 length filtered CDS sequences.Results showed that the content of GC at the third base of the genome codon of grain amaranth chloroplast was 27.31%,that is,the third codon was rich in A and U.ENC ranged from 35.25 to 61.00 meaning that the codon usage bias of most protein coding sequences was weak.There were 29 codons with relative synonymous codon usage greater than 1,of which 24 codons ending with A and T,indicating that the third codon preferred A and U.Neutrality analysis showed GC3 was significantly correlated with GC12,and the slope of regression curve was 0.403,which indicated that mutation had a great influence on codon bias.ENC-plot analysis revealed that most of the genes were located above and around the standard curve,indicating that natural selection also affected the formation of codon bias.Further correspondence analysis found that the first axis could explained 22.98%of variation,which was the major factor influencing codon bias.The first axis showed a significant correlation between ENC,whereas no significant correlation was found for GC3,CBI and GCall.The results of comprehensive analysis showed that mutation was the main factor affecting the codon bias in grain amaranth chloroplast genome,but other factors might also some influence,24 codons such as UUU,UUA and UCU were the optimal codons in Amaranthus hypochondriacus chloroplasts.