基于二代测序哈巴乌头叶绿体基因组分析  

Analysis of Chloroplast Genome based on Second-generation Sequencing of Aconitum habaense

作　　者：马福仙 魏健生 耿云芬 张汉尧[1] MA Fu-xian;WEI Jian-sheng;GENG Yun-fen;ZHANG Han-yao(Key Laboratory of Biodiversity Conservation in Southwest China,State Forestry Administration,Southwest Forestry University,Kunming Yunnan 650224,P.R.China;Yunnan Provincial Key Laboratory of Cultivation and Exploitation of Forest Plants,Conservation of Rare,Endangered&Endemic Forest Plants,Public Key Laboratory of the State Forestry Administration,Yunnan Academy of Forestry and Grassland,Kunming Yunnan 650201,P.R.China;Haba Snow Mountain Provincial Nature Reserve Management and Protection Bureau,Diqing Yunnan 674402,P.R.China)

机构地区：[1]西南林业大学西南地区生物多样性保育国家林业局重点实验室,云南昆明650224 [2]云南省林业和草原科学院云南省森林植物培育与开发利用重点实验室,国家林业局云南珍稀濒特森林植物保护和繁育重点实验室,云南昆明650201 [3]哈巴雪山省级自然保护区管护局,云南迪庆674402

出　　处：《西部林业科学》2023年第1期175-181,共7页Journal of West China Forestry Science

基　　金：昆明市国际(对外)科技合作基地(GHJD-2020031);云南省产业技术领军人才(YNWR-CYJS-2018-037);“气候变化影响下哈巴雪山珍稀濒危植物种质资源保存与人工繁育技术研究项目”共同资助。

摘　　要：为了解哈巴乌头叶绿体基因组特征及密码子偏好性,本研究采用Illumina HiSeq对哈巴乌头叶绿体基因组进行测序,组装获得完整叶绿体基因组序列,并利用CUSP和Codon W软件分析该物种叶绿体基因组密码子偏好性。结果显示:哈巴乌头叶绿体基因组全长155800 bp,是典型的四分结构,由1对长为29296 bp的IR、1个长为16864 bp的SSC和1个长86399 bp的LSC组成;该基因组包括84个蛋白质编码基因、8个rRNA基因和37个tRNA基因;系统进化分析显示,哈巴乌头和中甸乌头聚在同一个分支;叶绿体基因组密码子的3个位置上GC含量依次为GC1(46.65%)>GC2(39.71%)>GC3(29.01%),说明其偏好以A/U结尾;有效密码子数(ENC)范围为36.77~58.98,ENC值>45的编码序列有36个,说明密码子偏性低;中性绘图等分析显示哈巴乌头叶绿体基因组密码子偏好性受选择的影响较大;最优密码子有14个,均以A/U结尾。本研究为哈巴乌头叶绿体基因工程、种源鉴定等研究提供参考依据。In order to understand the chloroplast genome characteristics and codon usage bias of Aconitum habaense,the chloroplast genome of A.habaense was sequenced by Illumina HiSeq,the complete chloroplast genome sequence was obtained by assembly,CUSP and Codon W software was used to analyze the codon usage bias of the chloroplast genome.The results showed that the total length of the chloroplast genome was 155800 bp,which had a typical tetrad structure,consisting of a pair of IR(29296 bp),a SSC(16864 bp)and a LSC(86399 bp).The genome includes 84 protein-coding genes,8 rRNA genes and 37 tRNA genes.Phylogenetic analysis showed that A.habaense and A.piepunense clustered in the same clade.The GC content in the three positions of the chloroplast genome codon was GC1(46.65%)>GC2(39.71%)>GC3(29.01%)successively,indicating that it prefer ends with A/U.The range of effective number condon was from 36.77 to 58.98,and there were 36 coding sequence when ENC value was greater than 45,showing that the codon bias was weak.The neutrality plot and other analyses showed that the codon usage bias in the chloroplast genome of A.habaense was mainly affected by selection.The optimal codons had 14,all ending with A/U.The present study could be useful in the chloroplast genetic engineering and provenance identification of A.habaense.

关 键 词：哈巴乌头 Illumina测序 叶绿体基因组 密码子偏好性 

分 类 号：S567.239[农业科学—中草药栽培]