落葵叶绿体基因组特征分析  

Analysis of the Complete Chloroplast Genome of Basella alba

作　　者：杨世涵 王依霖 张怡 田玉肖 李梦瑶 陈清[1] 张芬[1] 孙勃[1] YANG Shihan;WANG Yilin;ZHANG Yi;TIAN Yuxiao;LI Mengyao;CHEN Qing;ZHANG Fen;SUN Bo(College of Horticulture,Sichuan Agricultural University,Chengdu 611130,China)

机构地区：[1]四川农业大学园艺学院,成都611130

出　　处：《四川农业大学学报》2024年第3期529-539,共11页Journal of Sichuan Agricultural University

基　　金：国家自然科学基金(32372732、32072586);四川省青年科学基金(2022NSFSC1689);四川农业大学本科生科研兴趣培养计划项目(2015009)。

摘　　要：【目的】落葵(Basella alba)为落葵科落葵属缠绕茎生草本植物,原产于中国和印度。植物叶绿体基因组遗传稳定,常被用于植物的鉴定及系统发育研究,旨在对落葵的叶绿体基因组进行特征分析。【方法】采用15对叶绿体基因组通用引物对落葵新鲜叶片提取的DNA进行扩增,并利用Illumina HiSeq X Ten平台进行测序,获得其叶绿体基因组序列。【结果】落葵叶绿体基因组全长156 533 bp,具有典型的四分体结构,包含83个编码蛋白基因、28个tRNA基因以及4个rRNA基因。检测到基因组中45个重复序列和263个简单重复序列,二核苷酸序列均为碱基AT/AT重复。密码子分析表明落葵叶绿体基因组密码子第三位碱基偏好使用A或U,综合中性绘图分析、ENC标准曲线分析、PR2-plot分析发现落葵叶绿体基因组密码子偏好性受自然选择因素为主的多种因素共同影响,符合落葵为双子叶植物的形态学分类结果。【结论】落葵与落葵薯叶绿体基因组高度相似,比较基因组学分析显示落葵与其他石竹目物种在反向重复区的收缩与扩张上存在差异。基于落葵在内的20种不同植物叶绿体基因组matK基因序列进行系统发育分析,结果表明落葵与其他落葵科植物处于同一进化分支,但其属间进化关系与形态学分类存在一定差异。研究结果为落葵科的资源分析及利用研究提供了理论基础。【Objective】Basella alba is a twining herbaceous plant of the genus Basella in the family Basellaceae,native to China and India.The plant chloroplast genome is genetically stable and is often used for plant identification and phylogenetic research.This study aims to analyze the characteristics of the chloroplast genome of B.alba.【Method】To sequencing the complete chloroplast genome of B.alba,the DNA of B.alba was extracted from fresh leaves,15 pairs of universal primer were used for PCR amplifications,and the complete chloroplast genome of B.alba was sequenced on a Hiseq X Ten platform.【Result】The chloroplast genome was 156533 bp in length and exhibited a typical tetrad structure,that contains 83 protein-coding genes,28 tRNA,and 4 rRNA.A total of 20 pairs of repeats and 262 SSR loci were identified,and only A/T type contained in mononucleotide repeats.Codon analysis showed that the third base of the codon in the chloroplast genome of B.alba prefers to use A or U.Through comprehensive neutral plot analysis,ENC standard curve analysis,and PR2-plot analysis,it was found that the codon preference in the chloroplast genome of lark is mainly influenced by multiple factors of natural selection,which is consistent with the morphological classification results of B.alba as a dicotyledonous plant.【Conclusion】The chloroplast genomes of B.alba and Anredera cordifolia are highly similar,and comparative genomics analysis shows that there are differences in the contraction and expansion of the reverse repeat region between B. alba and other Caryophyllales species. The phylogenetic analysis was carried out based on the matK gene sequences of 20 plant chloroplast genomes, and the results showed that B. alba and the other plants of Basellaceaes family were at the same evolutionary branches, but there still several differences in classification between morphological taxonomy and our results. Our results provide a theoretical basis for the resource analysis and utilization research of Basellaceaes.

关 键 词：落葵 叶绿体基因组 SSR 密码子偏好性 系统发育 

分 类 号：S636.9[农业科学—蔬菜学]