摘要
【目的】分析长尖叶蔷薇(Rosa longicuspis)的叶绿体基因组特征,为蔷薇属植物的分类鉴定、遗传变异分析以及系统发育关系研究提供科学依据。【方法】采用Illumina NovaSeq测序平台,对长尖叶蔷薇进行基因组重测序,并组装其叶绿体基因组。借助GeSeq在线平台,绘制其叶绿体基因组图谱和基因功能注释。利用MISA2.1、CodonW 1.4.2和MEGA 6.06等软件,对长尖叶蔷薇叶绿体基因组基本结构和功能进行分析。【结果】长尖叶蔷薇叶绿体基因组是四分体结构,长度为156659 bp。通过注释分析,共识别出140个基因,分别是蛋白质编码基因(92个)、rRNA基因(8个)和tRNA基因(40个),GC含量占比较高(37.22%)。长尖叶蔷薇的叶绿体基因组中,有一些基因包含内含子,这些基因主要分为两类:一类是含有1个内含子的基因,共有8个;另一类是含有2个内含子的基因,数量为3个。此外,在基因组中存在20个基因的重复现象,这些重复基因主要集中在反向重复区域;光合作用信号转导途径相关的基因(44个),参与核糖体大、小亚基构成的基因(21个)均为蛋白质编码基因。长尖叶蔷薇叶绿体基因组中含有57个SSR位点,共2种类型。长尖叶蔷薇的叶绿体基因组中,总共发现31种偏好密码子。在这些密码子中,有13种以碱基A结尾,16种以碱基U结尾,而以碱基G和碱基C结尾的密码子各自仅有1种。系统发育分析结果显示,长尖叶蔷薇和毛萼蔷薇的亲缘关系最近,聚合在一个分支上。‘月月粉’作为外类群,但没有单独形成1个分支,表明古老月季母性遗传相对稳定。【结论】长尖叶蔷薇叶绿体基因组具有高度保守的结构,注释得到的基因主要与光合作用和自我复制相关,以碱基A或碱基U结尾是长尖叶蔷薇叶绿体基因组的密码子偏好。分析得到的SSR大多为单核苷酸SSRs,系统发育分析表明长尖叶蔷薇与毛萼蔷薇的亲缘关系最近。本研究结果为蔷薇属植物的物种分类和亲缘关系分析提供了理论参考。
【Objective】The chloroplast genome characteristics of Rosa longicuspis were analyzed to provide scientific basis for taxonomic iden⁃tification,genetic variation analysis and phylogenetic relationship studies of Rosa.【Method】The chloroplast genome of R.longicuspis was as⁃sembled upon completion of the genome re⁃sequencing using the Illumina NovaSeq sequencing platform.The chloroplast genome map was drawn and gene function was annotated using the GeSeq online platform.Bioinformatics software such as MISA2.1,CodonW1.4.2,MEGA 6.06 were used to analyze the basic structure and function of the chloroplast genome of R.longicuspis.【Result】The chloroplast genome of R.longicuspis displayed a four⁃part structure and extended to 156659 bp in length.Annotation revealed a total of 140 genes,including 40 tRNA genes,8 rRNA genes and 92 protein⁃coding genes,with a relatively high GC content(37.22%).The chloroplast genome of R.longicuspis contained intron⁃containing genes,including 8 genes with 1 intron and 3 genes with 2 introns,as well as 20 duplicated genes located in the in⁃verted repeat region(IR).The photosynthetic signaling pathway involved 44 protein⁃coding genes,and 21 protein⁃coding genes were involved in the formation of ribosomal large and small subunits.The chloroplast genome of R.longicuspis contained 57 SSR loci of 2 types.A total of 31 preferred codons were identified in the chloroplast genome of R.longicuspis,of which 13 ended with A,16 ended with U,and only 1 each en⁃ded with G and C.According to phylogenetic study,R.longicuspis was most closely related to R.lasiosepala,clustering on the same branch.As an outgroup,R.chinensis‘Old Blush’did not form a separate branch,suggesting that maternal inheritance remained relatively stable in ancient roses.【Conclusion】R.longicuspis's chloroplast genome exhibits a highly conserved structure,with annotated genes primarily associat⁃ed with photosynthesis and self⁃replication.Codons ending with A or U are preferred in its chloroplast genome.Most identified SSRs are mono⁃nucleotide repeats.Phylogenetic analysis indicates the closest relationship between R.longicuspis and R.lasiosepala.These findings provide theoretical references for species classification and phylogenetic analysis of Rosa.
作者
周忠发
王川艺
刘萱
李淑斌
唐开学
ZHOU Zhong-fa;WANG Chuan-yi;LIU Xuan;LI Shu-bin;TANG Kai-xue(College of Agronomy and Biotechnology,Yunnan Agricultural University,Kunming 650100,China;National Engineering Research Center for Ornamental Horticulture,Flower Research Institute,Yunnan Academy of Agricultural Sciences,Kunming 650231,China;Yunnan Irose Horticultural Science and Technology Co.,Ltd.,Kunming 650600,China)
出处
《西南农业学报》
北大核心
2025年第6期1200-1208,共9页
Southwest China Journal of Agricultural Sciences
基金
云南省科技计划项目(202001AS07007)。
