Chloroplast Whole Genomes of Nine Hypericum Species： Genome Structure， Comparative Analysis， and Phylogenetic Relationships

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

Abstract

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

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.

Figures/Tables 9

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)

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

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

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

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

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

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

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

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

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