摘要
[目的]全面解析鸡骨柴(Elsholtzia fruticosa)的叶绿体全基因组序列与结构特征,探讨香薷属药用植物叶绿体基因组的整体特征与变异模式,比较序列的种间变异情况,筛选种间高变异序列,为香薷属药用植物叶绿体基因组的深入研究和应用奠定基础。[方法]以传统民族药用植物鸡骨柴为试验材料,采用高通量测序技术对鸡骨柴进行叶绿体基因组测序、组装和注释,同时利用生物信息学手段对4种香薷属药用植物(鸡骨柴、海州香薷、密花香薷、边山香薷)叶绿体基因组的反向重复区边界、结构同源性、基因密码子使用偏性参数、核苷酸组成及进化关系进行分析。[结果](1)鸡骨柴叶绿体基因组全长151550 bp,为典型四分体结构,共检测出49个简单重复序列(SSRs)。(2)4种香薷属药用植物叶绿体基因组边界扩张收缩较为稳定相似,只在个别种(密花香薷、边山香薷)中发生了较小变异。(3)4种香薷属药用植物的非编码区变异大于编码区,同时大单拷贝区的变异程度最高,反向重复区a的变异程度最低。(4)相对于其它3个物种,鸡骨柴叶绿体基因组变异程度最低,psbA、petA、psbF、ycf1、petG和psbL等基因编码区存在显著差异,同时trnQ-UUG、trnS-GCT、trnM-GTT、trnS-GGA、trnL-CAA等基因间隔区也存在不同程度的变异。(5)4种香薷属药用植物叶绿体基因组密码子偏好性主要受碱基突变和选择压力的影响,最优密码子大多以A或T(U)作为第3位碱基。(6)系统发育树表明鸡骨柴与野拔子亲缘关系最近。[结论]本研究为香薷属药用植物的系统发育研究和分子标记开发等工作提供了参考依据。
[Objective]In order to comprehensively analyze the complete chloroplast genome sequence and structural characteristics of Elsholt-zia fruticosa,the article discussed the overall characteristics and variation patterns of the chloroplast genome of the medicinal plant Elsholt-zia.The interspecific variation of the sequence was compared and the high variation sequence was screened,which laid a foundation for the in-depth study and application of the chloroplast genome of Elsholtzia medicinal plants.[Method]The chloroplast genome of the traditional ethnomedicinal plant E.fruticosa was sequenced,assembled,and annotated using high-throughput sequencing technology.At the same time,softwares such as MISA-web were used to analyze the IR limit,codon usage preference parameters,nucleotide composition and evolu-tionary relationship of the chloroplast genome of four Elsholtzia medicinal plants(E.fruticosa,E.splendens,E.densa,E.byeonsanensis).[Result](i)The total length of the chloroplast genome was 151550 bp,with a typical tetrad structure and 49 simple sequence repeats(SSRs)detected.(i)The expansion and contraction of the chloroplast genome boundary of the four medicinal plants of Elsholtzia were rela-tively stable and similar,and only small variations had occurred in individual species(E.splendens,E.byeonsanensis).(ii)The differ-ences between the non-coding regions of the four Elsholtzia medicinal plants were greater than that of the coding region.At the same time,the large single copy region(LSC)had the highest degree of variation,and the inverted repeat region(IRa)had the lowest degree of varia-tion.(iv)Compared with the other three species,the chloroplast genome of E.fruticosa had the lowest degree of variation.There were sig-nificant differences in the coding regions of psbA,petA,psbF,ycfl,petG and psbL.At the same time,intergenic regions such as trnQ-UUG,trnS-GCT,trnM-GTT,trnS-GGA,and trnL-CAA also showed varying degrees of variation.(v)Codon bias in the chloroplast genomes of four medicinal plants of Elsholtzia was mai
作者
余潇
宋雨茹
赵振宁
YU Xiao;SONG Yu-ru;ZHAO Zhen-ning(School of Economic Geography,Hunan University of Finance and Economics,Changsha 410205,China;Hunan University of Finance and Economics,Hunan Institute of Economic Geography,Changsha 410205,China;College of Landscape Architecture and Horticulture,Southwest Forestry University,Kunming 650224,China;College of Forestry,Southwest Forestry University,Kunming 650224,China)
出处
《西南农业学报》
CSCD
北大核心
2024年第7期1420-1434,共15页
Southwest China Journal of Agricultural Sciences
基金
湖南财政经济学院博士科研启动资金项目(90174010191)
云南省第二次国家重点保护野生植物资源调查项目(09930-216304)
2021年度云南省大学生创新创业国家级项目(202110677046)。
关键词
鸡骨柴
香薷属
叶绿体基因组特征
密码子偏好性
系统发育分析
Elsholtzia fruticosa
Elsholtzia
Chloroplast genome characteristics
Code usage bias
Phylogenetic analysis
