九种金丝桃属植物叶绿体全基因组：基因组结构、比较分析和系统发育关系

doi:10.13560/j.cnki.biotech.bull.1985.2025-1253

摘要/Abstract

摘要：

目的分析川滇金丝桃（Hypericum forrestii）在内的金丝桃属物种叶绿体基因组结构、基因组成及系统发育关系，为物种鉴定和进化研究提供基因组学基础。方法采用高通量测序技术对川滇金丝桃叶绿体基因组进行测序与组装，并结合NCBI数据库获取的8种金丝桃属已发表叶绿体基因组数据，共计9个物种开展比较基因组学分析。利用相关生物信息学工具对叶绿体基因组进行基因注释，并进一步开展简单重复序列（SSR）分析、密码子使用偏好分析、IR边界结构比较以及核苷酸多样性分析，同时基于完整叶绿体基因组序列构建系统发育树。结果对9种金丝桃属植物的叶绿体基因组进行分析，结果表明，所有物种的基因组结构均呈典型的四分体环状结构，基因数在110-130个之间，符合已报道的金丝桃属叶绿体基因组特征。基因组长度范围为122 570-168 150 bp，GC含量为37.04%-38.14%。SSR分析表明，单核苷酸重复类型占主导，且以A/T碱基为主。密码子使用分析表明，A/U结尾的密码子使用偏好性明显。核苷酸多样性分析显示，LSC和SSC区域为主要的变异热点，尤其是trnH-psbA、rpoC2-rpoC1、ndhF-rpl32等基因间区。系统发育分析表明，金丝桃属为单系群，支持与川苔草科的亲缘关系。结论 9种金丝桃属植物叶绿体基因组均呈典型四分体结构，IR区的动态变化是导致基因组长度差异的主要因素，LSC和SSC区的高变异热点区域可作为潜在的分子标记。系统发育分析支持金丝桃属为单系群，并与川苔草科具有较近亲缘关系。

关键词: 川滇金丝桃, 叶绿体基因组, 系统发育分析, 比较基因组学, 简单重复序列（SSR）, 核苷酸多样性, IR边界

Abstract:

Objective This study aimed to analyze the chloroplast genome structure, gene composition, and phylogenetic relationships of Hypericum forrestii and related Hypericum species, providing a genomic foundation for species identification and evolutionary research. Method The chloroplast genome of H. forrestii was sequenced and assembled using high-throughput sequencing technology. Together with sequences of eight published Hypericum species retrieved from the NCBI database, a total of nine chloroplast genomes were analyzed. Comparative genomic analyses were performed, including genome annotation, simple sequence repeat (SSR) identification, codon usage bias analysis, inverted repeat (IR) boundary comparison, nucleotide diversity analysis, and phylogenetic reconstruction based on complete chloroplast genome sequences. Result The chloroplast genomes of the nine Hypericum species exhibited a typical quadripartite circular structure, with gene numbers ranging from 110 to 130, consistent with previously reported features in the genus. Genome sizes ranged from 122 570 to 168 150 bp, with GC content of 37.04%-38.14%. SSR analysis showed that single nucleotide repeat were dominant, and mononucleotide A/T repeats were the most abundant repeat type. Codon usage analysis showed a clear preference for A/U-ending codons. Nucleotide diversity analysis indicated that the LSC and SSC regions were the primary variation hotspots, particularly the intergenic spacers trnH-psbA, rpoC2-rpoC1, and ndhF-rpl32. Phylogenetic analysis supported the monophyly of Hypericum and its close relationship with Podostemaceae. Conclusion The chloroplast genomes of nine Hypericum species all exhibit a typical quadripartite structure. Dynamic changes in the IR regions are the main mechanism responsible for genome size variation, while highly variable hotspots in the LSC and SSC regions serve as promising molecular markers. Phylogenetic analysis supports the monophyly of Hypericum and its close relationship with Podostemaceae.

Key words: Hypericum forrestii, chloroplast genome, phylogenetic analysis, comparative genomics, simple sequence repeats (SSRs), nucleotide diversity, IR boundary

范照睿, 王佳敏, 童凯, 康振辉. 九种金丝桃属植物叶绿体全基因组：基因组结构、比较分析和系统发育关系[J]. 生物技术通报, 2026, 42(10): 216-228.

FAN Zhao-rui, WANG Jia-min, TONG Kai, KANG Zhen-hui. Chloroplast Whole Genomes of Nine Hypericum Species： Genome Structure， Comparative Analysis， and Phylogenetic Relationships[J]. Biotechnology Bulletin, 2026, 42(10): 216-228.

图/表 9

图1 川滇金丝桃叶绿体基因组图谱图中展示了4个基因组区域（大单拷贝区LSC、小单拷贝区SSC、反向重复区IRA和反向重复区IRB）。圆内的基因顺时针转录，圆外的基因逆时针转录。不同功能类别的基因用不同颜色标记。内圈显示GC含量（深灰色）和AT含量（浅灰色）

Fig. 1 Chloroplast genome map of Hypericum forrestiiThe figure shows four genomic regions: the Large Single-Copy region (LSC), the Small Single-Copy region (SSC), and the two Inverted Repeat regions (IRA and IRB). Genes located inside the circle are transcribed clockwise, while those outside are transcribed counter clockwise. Genes belonging to different functional categories are marked in different colors. The inner circle indicates the GC content (dark gray) and AT content (light gray)

图2 9种金丝桃属植物叶绿体基因组的SSR位点分析A-I：在不同重复类型中识别出的SSR基序的频率

Fig. 2 Analysis of SSR loci in the chloroplast genomes of nine Hypericum speciesA-I: Frequency of SSR motifs identified in different repeat types

图3 SSR位点在LSC、SSC和IR区域内的重复类型频率

Fig. 3 Frequency of SSR repeat types in the LSC, SSC, and IR regions

图4 9种金丝桃属植物的长重复序列数和类型图中蓝色条状P代表回文重复序列，橙色条状F代表正重复序列，绿色条状C代表互补重复序列，红色条状R代表反向重复序列

Fig. 4 Number and types of long repeat sequences in nine Hypericum speciesThe blue bars labeled P represent palindromic repeats, the orange bars labeled F represent forward repeats, the green bars labeled C represent complementary repeats, and the red bars labeled R represent reverse repeats

图5 金丝桃属植物的相对同义密码子使用度（RSCU）A：9种金丝桃属植物不同密码子RSCU柱状图；B：9种金丝桃属植物RSCU值的热图

Fig. 5 Relative synonymous codon usage (RSCU) in Hypericum speciesA: Bar chart of RSCU for different codons across nine Hypericum species. B: Heatmap of RSCU values for nine Hypericum species

图6 9种金丝桃属叶绿体基因组中LSC、SSC和IR区域边界的比较

Fig. 6 Comparison of the boundaries of LSC, SSC, and IR regions in the chloroplast genomes of nine Hypericum species

图7 9种金丝桃属叶绿体基因组序列特征比较图谱x轴代表核苷酸序列，y轴代表序列同源性百分比，范围50%-100%。曲线下方突出显示了保守区域，红色区域为“保守非编码序列”（CNS），深蓝色区域为外显子，浅蓝色区域为tRNA或rRNA

Fig. 7 Comparative map of sequence features of the chloroplast genomes of nine Hypericum speciesThe x-axis represents the nucleotide sequence, and the y-axis represents the sequence homology percentage, ranging from 50% to 100%. Conserved regions are highlighted below the curve, with red indicating “Conserved Noncoding Sequences” (CNS), dark blue indicating exons, and light blue indicating tRNA or rRNA

图8 9种金丝桃属植物的全叶绿体基因组滑动窗口分析x轴：窗口中点的位置；y轴：每个窗口的核苷酸多样性；红色虚线代表9种植物叶绿体基因组的平均核苷酸多样性水平

Fig. 8 Sliding window analysis of the complete chloroplast genomes of nine Hypericum speciesx-axis: midpoint position of each window; y-axis: nucleotide diversity of each window. The red dashed line represents the average nucleotide diversity across the complete chloroplast genomes of the nine Hypericum species

图9 基于最大似然法（ML）构建的金虎尾目植物叶绿体基因组系统发育树

Fig. 9 Maximum likelihood phylogenetic tree of Malpighiales based on chloroplast genomes

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