摘要
为分析峨眉含笑叶绿体基因组密码子的使用偏性,揭示影响其密码子使用偏性的主要因素,首先从NCBI数据库中下载峨眉含笑叶绿体基因组完整序列,用于CDS序列筛选,然后利用CodonW 1.4.2和EMBOSS在线软件对峨眉含笑密码子的组成成分进行分析,从而得到GC含量、ENC、RSCU等参数,最后做中性、ENC和PR2绘图分析,研究导致密码子偏倚形成的主要原因,以期取得最优密码子。结果表明:峨眉含笑叶绿体基因组CDS序列的密码子在第三位上GC含量较低,平均值为31.26%。ENC为36.36~57.89,表明密码子的偏性较弱,ENC与GC2和GC3均呈极显著相关。有32个密码子的RSCU> 1,其中以G/C结尾的有3个,A/U结尾的有29个。中性绘图、ENC-plot和PR2-plot分析显示:由于选择压力的存在,使峨眉含笑叶绿体基因组密码子在一定程度上表现出偏好性使用。对应性分析显示:编码核糖体蛋白的基因位点分布比较零散,说明该类基因密码子的使用模式相差较大,在峨眉含笑叶绿体基因组中的表达率较高。该研究明确了峨眉含笑叶绿体基因组密码子使用偏性主要受选择压力的影响,并最终从峨眉含笑叶绿体基因组中筛选出UUU、CUU和UCU等14个最优密码子,且均以碱基A和U结尾。
The codon usage bias in chloroplast genome of Michelia wilsonii was analyzed to reveal the main factors affecting it.First,the whole sequence of the M.wilsoni chloroplast genome was downloaded from the NCBI database for CDS sequence screening.Then CodonW 1.4.2 and EMBOSS were used to analyze the codon composition of the M.wilsonii chloroplast genome,to obtain GC content,ENC,RSCU,and other related paramet-ers.Finally,neutral plot,ENC-plot,and PR2-plot analysis were performed to study the main factors of codon bi-as formation to obtain optimal codons.The results showed that the GC content of the third base of the codon in the chloroplast genome of M.wilsoni was low,with an average of 31.26%.ENC was between 36.36-57.89,indicating that the codon bias was weak,and ENC was significantly correlated with GC2 and GC.There were 32 codons with RSCU>1,3 with G and C bases,and 29 with A and U bases.Its neutral plot,ENC-plot,and PR2-plot analysis showed that the codon usage bias of the chloroplast genome of M.wilsonii was mainly influenced mainly by selection pressure.Correspondence analysis showed that the gene sites encoding ribosomal proteins were dispersed,and the usage patterns of these gene codons were quite different,indicating that the expression rate of these genes in chloroplast genes of M.wilsonii was high.This study clarified that the main factor is selection pressure affecting the bias of the chloroplast codon usage in the M.wilsonii chloroplast genome.Finally,14 optimal codons,including UUU,CUU,UCU,and so on,were selected from the chloroplast genome of M.wilsoni.They all end with bases A and U.
作者
朱令
王素杰
杨娜
蔡涵冰
尹拓
韩沛辰
张汉尧
Zhu Ling;Wang Sujie;Yang Na;Cai Hanbing;Yin Tuo;Han Peichen;Zhang Hanyao(Key Laboratory of Forest Genetic Improvement and Breeding,Southwest Forestry University,Kunming Yunnan 650233,China;The Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation of Southwest China,Southwest Forestry University,Kunming Yunnan 650233,China)
出处
《西南林业大学学报（自然科学）》
北大核心
2023年第4期89-99,共11页
Journal of Southwest Forestry University：Natural Sciences
基金
国家自然科学基金项目(32160556)资助。
