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<p><i>Ginkgo biloba</i> is a relict species of major phylogenetic and conservation significance. Previous studies have largely clarified the major lineage structure of <i>G. biloba</i> based on molecular evidence, particularly chloroplast genome data. However, recent field investigations identified a <i>Ginkgo biloba</i> population at Guniujiang, Anhui, and comprehensive observations suggested that this population has considerable research potential. In this study, six <i>G. biloba</i> samples from Guniujiang, Qingliangfeng, and Tianmu Mountain were analyzed using complete chloroplast genome assembly, comparative genomics, and phylogenetic reconstruction. All six chloroplast genomes exhibited the typical quadripartite circular structure and ranged from 156,938 to 157,009&#xa0;bp in length, with GC contents of 39.56–39.57%. Each genome contained 133 annotated genes, including 86 protein-coding genes, 39 tRNA genes, and 8 rRNA genes, and showed highly conserved gene content and genome organization. Codon usage showed a clear preference for A/T-ending synonymous codons. Comparative analyses indicated that overall genome structure, gene order, and IR/SC boundaries were highly conserved, whereas sequence variation was mainly concentrated in several non-coding regions. Sliding-window analysis revealed low overall nucleotide diversity (mean Pi = 0.00020) and detected 72 polymorphic sites, with the major divergence peaks located in <i>psb</i>A-<i>trn</i>K (exon 2), <i>trn</i>K (exon 2)-<i>mat</i>K, and <i>psb</i>K-<i>psb</i>I. In addition, 66 stable core SNPs were identified. Phylogenetic analysis based on 77 chloroplast genomes, including 71 published genomes and 6 newly generated genomes, showed that all six samples were placed within the <i>Ginkgo biloba</i> clade. Notably, the two Guniujiang samples, GNJYX2 and GNJYX5, were placed in a relatively distinct chloroplast branch, indicating detectable chloroplast-level differentiation. These results provide new plastome data for evaluating the phylogenetic affinity and chloroplast-level differentiation of the Guniujiang population and contribute to studies of genetic diversity, phylogeny, and conservation of <i>Ginkgo biloba</i>.</p>

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Chloroplast genomes and phylogenetic position of a Ginkgo biloba population from Guniujiang, a newly documented distribution site in Anhui, China

  • 期刊论文

  • 发表日期：

    2026年7月1日

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  • Shu Lin,
  • Wenhao Lu,
  • Chengwen Zhu,
  • Zhiyun Zhu,
  • Shuyuan Yao,
  • Yanfang Yang,
  • Kai Zhao

摘要

Ginkgo biloba is a relict species of major phylogenetic and conservation significance. Previous studies have largely clarified the major lineage structure of G. biloba based on molecular evidence, particularly chloroplast genome data. However, recent field investigations identified a Ginkgo biloba population at Guniujiang, Anhui, and comprehensive observations suggested that this population has considerable research potential. In this study, six G. biloba samples from Guniujiang, Qingliangfeng, and Tianmu Mountain were analyzed using complete chloroplast genome assembly, comparative genomics, and phylogenetic reconstruction. All six chloroplast genomes exhibited the typical quadripartite circular structure and ranged from 156,938 to 157,009 bp in length, with GC contents of 39.56–39.57%. Each genome contained 133 annotated genes, including 86 protein-coding genes, 39 tRNA genes, and 8 rRNA genes, and showed highly conserved gene content and genome organization. Codon usage showed a clear preference for A/T-ending synonymous codons. Comparative analyses indicated that overall genome structure, gene order, and IR/SC boundaries were highly conserved, whereas sequence variation was mainly concentrated in several non-coding regions. Sliding-window analysis revealed low overall nucleotide diversity (mean Pi = 0.00020) and detected 72 polymorphic sites, with the major divergence peaks located in psbA-trnK (exon 2), trnK (exon 2)-matK, and psbK-psbI. In addition, 66 stable core SNPs were identified. Phylogenetic analysis based on 77 chloroplast genomes, including 71 published genomes and 6 newly generated genomes, showed that all six samples were placed within the Ginkgo biloba clade. Notably, the two Guniujiang samples, GNJYX2 and GNJYX5, were placed in a relatively distinct chloroplast branch, indicating detectable chloroplast-level differentiation. These results provide new plastome data for evaluating the phylogenetic affinity and chloroplast-level differentiation of the Guniujiang population and contribute to studies of genetic diversity, phylogeny, and conservation of Ginkgo biloba.