南方农业学报2022，Vol.53Issue(9) ：2497-2509.DOI:10.3969/j.issn.2095-1191.2022.09.012

大旗瓣凤仙花与瑶山凤仙花叶绿体全基因组比较及系统发育分析

Phylogenetic analysis and comparison of the complete chloroplast genomes in Impatiens macrovexilla and I. macrovexilla var. yaoshanensis

陶大燕 宋倩 闫海霞 周锦业 关世凯 潘有强 罗述名
南方农业学报2022，Vol.53Issue(9) ：2497-2509.DOI:10.3969/j.issn.2095-1191.2022.09.012
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  • 维普
  • 万方数据

大旗瓣凤仙花与瑶山凤仙花叶绿体全基因组比较及系统发育分析

Phylogenetic analysis and comparison of the complete chloroplast genomes in Impatiens macrovexilla and I. macrovexilla var. yaoshanensis

陶大燕 1宋倩 1闫海霞 1周锦业 1关世凯 1潘有强 2罗述名3
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作者信息

  • 1. 广西农业科学院花卉研究所,广西南宁 530007
  • 2. 广西作物遗传改良生物技术重点开放实验室,广西南宁 530007
  • 3. 广西农业科学院花卉研究所,广西南宁 530007;悉尼大学农业与环境学院植物育种研究所,澳大利亚新南威尔士州 2570
  • 折叠

摘要

[目的]比较大旗瓣凤仙花和瑶山凤仙花的叶绿体全基因组序列,并分析凤仙花属20个物种的系统发育情况及遗传进化关系,为证实这两个分类群的早期植物学分类及其种质资源利用和遗传改良提供理论依据.[方法]基于BGISEQ-500测序平台,对大旗瓣凤仙花和瑶山凤仙花叶绿体基因组进行测序,利用Fastp软件和NOVOPlasty v.2.6.2程序对叶绿体基因组进行组装.利用CpGAVAS在线工具对叶绿体基因组序列进行注释,并使用MAFFT v.7.0、CAIcal、REPuter、MISA和FastTree等生物信息学软件进行序列比对、密码子偏性分析、重复序列定位及简单重复序列(SSRs)和系统发育分析.[结果]大旗瓣凤仙花和瑶山凤仙花叶绿体基因组长度分别为152437和152286 bp,GC含量分别为36.77％和36.80％;其中大单拷贝(LSC)区分别为83331和83212 bp,小单拷贝(SSC)区分别为17376和17312 bp,反向重复区(IRa和IRb)分别为25865和25881 bp.大旗瓣凤仙花和瑶山凤仙花叶绿体基因组均包含88个蛋白编码基因、8个rRNA基因和37个tRNA基因,且无假基因.系统发育分析结果表明,凤仙花属内的物种分类与基于系统形态学分析的早期植物学分类一致;虽然大旗瓣凤仙花和瑶山凤仙花叶绿体基因组非常接近,但二者为不同的凤仙花属种类,而不是早期形态分类学上的两个亚种水平.[结论]大旗瓣凤仙花和瑶山凤仙花为2个独立的凤仙花属种类,二者叶绿体基因组发生部分遗传变异,鉴定出的SSRs位点可用于物种鉴定和群体遗传学研究.

Abstract

This research sequenced the complete chloroplast genome of Impatiens macrovexilla and I. macrovexilla var. yaoshanensis,so as to compare and analyze their differences in genome structure,and to construct the phylogenetic relationships of 20 Impatiens species. The phylogenetic results would provide basis for further confirming earlier botanical classifications of these two taxa,as well as benefiting the application and genetic improvement of germ-plasm resources.[Method]The genomic DNA of I. macrovexilla and I. macrovexilla var. yaoshanensis were sequenced by using the BGISEQ-500 platform. The Fastp software and the NOVOPlasty v.2.6.2 program were used to assemble the final chloroplast genome. The chloroplast genomes were annotated with the CpGAVAS online tool;the other bioinformatics software including MAFFT v.7.0,CAIcal,REPuter,MISA,and FastTree were used for sequence alignment,relative synon-ymous codon usage(RSCU)for the protein-coding genes,location of the repeat sequences,the simple sequence repeats (SSRs)and a maximum likelihood(ML)phylogenetic trees.[Result]The established circular genome of I. macrovexilla and I. macrovexilla var. yaoshanensis had 36.77％and 36.80％of GC contents,which contained 152437 and 152286 bp,re-spectively. These two genomes included a large single-copy(LSC)region of 83331 and 83212 bp,a small single-copy (SSC)region of 17376 and 17312 bp,and a pair of inverted repeats(Ira and Irb)of 25865 and 25881 bp,respectively.Both of two genomes presented with 88 protein-coding genes,8 Rrna genes,37 Trna genes and no pseudogenes. The phylogenetic dendrogram analysis revealed that,species classification within the genus Impatiens were consistent with the earlier botanical classification based on systematic morphological analysis. Even though the chloroplast of I. macrovexilla and I. macrovexilla var. yaoshanensis were genetically very close,they formed two distinct species rather than the subspe-cies level proposed by former botanists.[Conclusion]I. macrovexilla and I. macrovexilla var. yaoshanensis would be se-parated as two individual species. Some genetic variation in chloroplast,especially the identified SSR loci can be used for species identification and population genetics studies.

关键词

大旗瓣凤仙花/瑶山凤仙花/叶绿体全基因组/系统发育

Key words

Impatiens macrovexilla/Impatiens macrovexilla var. yaoshanensis/chloroplast genome/phylogenetic analysis

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基金项目

出版年

2022
南方农业学报
广西壮族自治区农业科学院

南方农业学报

CSTPCDCSCD北大核心
影响因子：0.83
ISSN：2095-1191
参考文献量1
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