榆叶梅叶绿体基因组特征分析
Analysis of the Chloroplast Genomic Characterization in Amygdalus triloba
段春燕 1董庆林 2胡一浩 2王晓凌1
作者信息
- 1. 河南科技大学农学院,河南 洛阳 471000;河南科技大学牡丹学院,河南 洛阳 471000
- 2. 河南科技大学农学院,河南 洛阳 471000
- 折叠
摘要
[目的]对榆叶梅(Amygdalus triloba)叶绿体基因组进行特征分析,并依据基因组序列数据构建系统发育树.[方法]通过Illumina HiSeq X Ten平台对榆叶梅叶绿体基因组进行序列测序、组装和基因注释,用生物信息学分析方法对其叶绿体基因组进行特征解析.[结果]研究发现榆叶梅叶绿体基因组大小和结构与经典被子植物相似.其蛋白编码基因共编码24 930个密码子,有29个偏好密码子.其中,亮氨酸密码子数目最多,占总量的10.56%.根据设置参数,发现榆叶梅叶绿体基因组中串联重复有15个.SSR(简单重复序列)大多位于基因间区IGS和LSC区域,位点有32个.[结论]榆叶梅与同亚属长柄扁桃(Amygdalus pedunculata)和李属(Prunus)毛樱桃(Prunus tomentosa)亲缘关系较近,但与同亚属的扁桃(Amygdalus dulcis)亲缘关系较远.
Abstract
[Objective]This study aims to analyze the characteristics of the chloroplast genome of Amyg-dalus triloba and construct a phylogenetic tree based on the chloroplast genome sequence data.[Method]The chloroplast genome of A.triloba was sequenced using Illumina HiSeq X Ten sequencing platform,and sequence assembly and annotation were performed.Bioinformatics analysis methods were employed to analyze the characteristics of the chloroplast genome.[Result]The results indicated that the chloroplast genomic size and structure of A.triloba were comparable to those of typical angio-sperm plants.The protein coding genes encodes a total of 24 930 codons,with 29 preferred codons.Among them,the highest number of codons encoding leucine accounting for 10.56%of the total.Fifteen tandem repeats were identified in the chloroplast genome of A.triloba based on specified parameters.Simple repeating sequence(SSR)with 32 loci were predominantly located in the IGS and LSC regions.[Conclusion]Phylogenetic analysis revealed a close relationship between A.triloba and the same subge-nus of Amygdalus pedunculata and the Prunus genus of Prunus tomentosa,while showing a distant rela-tionship with the same subgenus of Amygdalus dulcis.
关键词
榆叶梅/叶绿体基因组/生物信息学/密码子偏好性/重复序列/系统发育Key words
Amygdalus triloba/chloroplast genome/bioinformatics/codon preference/repeated sequence/phylogeny引用本文复制引用
基金项目
国家自然科学基金(U1304326)
河南省特色骨干学科建设项目(17100001)
河南科技大学大学生研究训练计划(SRTP)项目(2024537)
河南科技大学博士科研启动基金项目(4024-13480114)
出版年
2024
NETL
NSTL
万方数据