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<p>The Annonaceae is characterized by its high species diversity and significant morphological variation. Owing to their conserved nature, plastid genomes (plastomes) are widely used in phylogenetic research. To elucidate the evolutionary patterns of plastomes within the Annonaceae, this study employed next-generation sequencing technology to sequence and structurally analyze the plastomes of <i>Orophea hainanensis</i>. The genome exhibits a typical circular quadripartite structure, with a total length of 160,411&#xa0;bp and a GC content of 39.1%. The sizes and GC contents of the large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) regions are 89,367 bp (37.6%), 18,934&#xa0;bp (34.3%), and 26,055&#xa0;bp&#xa0;(43.4%), respectively. Annotation identified 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Repetitive sequence analysis revealed the presence of 51 simple sequence repeats, 38 tandem repeats, and 49 dispersed repeats. Codon usage bias analysis identified 29 high-frequency codons and 5 optimal codons, all of which ended with A/T. The plotting results indicated that natural selection is the predominant factor shaping codon usage bias. Phylogenetic analysis demonstrated that <i>O. hainanensis</i> forms a sister group with <i>Miliusa glochidioides</i>, while the subfamilies Annonoideae and Malmeoideae constitute a monophyletic clade. The subfamilies Ambavioideae and Anaxagoreoideae are positioned successively at the base of the phylogenetic tree. This study unveils the evolutionary characteristics of the plastome in <i>O. hainanensis</i> and provides a crucial molecular foundation for future conservation genetic research on this species.</p>

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Plastome structure, repetitive sequences, and phylogeny of Orophea hainanensis (Annonaceae)

  • 期刊论文

  • 发表日期：

    2026年3月13日

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  • Jingyao Ping,
  • Dong Tan,
  • Aimin Li,
  • Yangying Gan,
  • Xianhai Zeng

摘要

The Annonaceae is characterized by its high species diversity and significant morphological variation. Owing to their conserved nature, plastid genomes (plastomes) are widely used in phylogenetic research. To elucidate the evolutionary patterns of plastomes within the Annonaceae, this study employed next-generation sequencing technology to sequence and structurally analyze the plastomes of Orophea hainanensis. The genome exhibits a typical circular quadripartite structure, with a total length of 160,411 bp and a GC content of 39.1%. The sizes and GC contents of the large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) regions are 89,367 bp (37.6%), 18,934 bp (34.3%), and 26,055 bp (43.4%), respectively. Annotation identified 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Repetitive sequence analysis revealed the presence of 51 simple sequence repeats, 38 tandem repeats, and 49 dispersed repeats. Codon usage bias analysis identified 29 high-frequency codons and 5 optimal codons, all of which ended with A/T. The plotting results indicated that natural selection is the predominant factor shaping codon usage bias. Phylogenetic analysis demonstrated that O. hainanensis forms a sister group with Miliusa glochidioides, while the subfamilies Annonoideae and Malmeoideae constitute a monophyletic clade. The subfamilies Ambavioideae and Anaxagoreoideae are positioned successively at the base of the phylogenetic tree. This study unveils the evolutionary characteristics of the plastome in O. hainanensis and provides a crucial molecular foundation for future conservation genetic research on this species.