西南林业大学学报2025，Vol.45Issue(7)：72-80,9.DOI:10.11929/j.swfu.202410002
民族药象牙参属叶绿体基因组密码子偏好性分析
Analysis on Codon Usage Bias of Chloroplast Genome in the Ethnic Medicine of Roscoea
摘要
Abstract
In order to explore the preference and influencing factors of codon usage in the chloroplast genome of plants in the genus Roscoea,this study collected chloroplast genomes of 3 species of Roscoea,and calculated codon composition parameters using Codon W and CUSP software.Based on this data,ENC-plot,RP2-plot,neutral plot and additional analyses were conducted.The results showed that the codon usage patterns in the chloroplast genomes of 3 species of plants in Roscoea were mostly the same,with a preference ending in A/U.The ENC values of protein coding genes in all 3 species of plants were greater than 35.This indicates that the codon preference in the Roscoea is weak.The results of neutral plot,ENC-Plot and PR2-Plot analysis all show that natural selection is the main factor affecting the codon preference of Roscoea.The optimal codons for Roscoea tibetica,Roscoea humeana,Roscoea alpina were screened out at 9,11 and 12,with a total of 6 codons,namely CUU,UCA,ACA,GCA,UAA and AGA,indicating that the codon usage pattern of the chloro-plast genome in Roscoea is predominantly affected by the combination of mutation pressure and positive selection.关键词
叶绿体基因组/象牙参属/密码子偏好性/最优密码子Key words
chloroplast genome/Roscoea/codon usage bias/optimal codon分类
生物科学引用本文复制引用
赵飞亚,刘星雨,张捷,陶爱恩..民族药象牙参属叶绿体基因组密码子偏好性分析[J].西南林业大学学报,2025,45(7):72-80,9.基金项目
云南省科技厅基础研究计划面上项目(202101AT070001)资助 （202101AT070001）
云南省大学生创新创业训练计划项目(SC20201332804、SC20211332803、SC202213328004)资助 （SC20201332804、SC20211332803、SC202213328004）
丽江市科技计划项目(2022LJSHFZ010)资助 （2022LJSHFZ010）
丽江市中青年学术和技术带头人后备人才项目资助. （）
