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Background <p>Current research on the Styracaceae family is limited by the number of sampled genera and species, and the comparative analysis of their chloroplast genomes, as well as phylogenetic studies, are quite restricted.</p> Results <p>This study conducted a comprehensive comparative analysis of the chloroplast genomes of the Styracaceae family, covering 52 species from 12 genera. Genomic variations occurred mainly among genera but were conserved within each genus. In the specific lineages (<i>Bruinsmia</i>, <i>Alniphyllum</i>, <i>Melliodendron</i>, and <i>Huodendron</i>) of this family, there were cases of fragment insertion or deletion in several genes (<i>accD</i>, <i>clpP</i>, <i>rpoB</i>, <i>rps16</i>, and <i>ycf15</i>), with gene loss or intron loss observed in <i>Bruinsmia</i> (<i>rpoB</i> or <i>rps16</i>, and <i>clpP</i>), <i>Alniphyllum</i> (<i>clpP</i>), and <i>Huodendron</i> (<i>clpP</i> and <i>ycf15</i>). The inverted repeat regions of the genus <i>Melliodendron</i> showed slight contractions. The nucleotide diversity (Pi) of the protein-coding sequences (CDSs) was studied, and six CDSs with Pi values greater than 0.03 were screened out as candidate molecular markers for further phylogenetic research of the family globally. The positive selection analysis indicated that a total of twenty genes were under strong positive selection, while six genes were under weak positive selection. This study determined the phylogeny position of the genus <i>Parastyrax</i>, but leaves the relationships among Clades B (<i>Sinojackia</i>, <i>Pterostyrax</i>, and <i>Halesia carolina</i>), C (<i>Melliodendron</i> and <i>Changiostyrax</i>), and D (<i>Rehderodendron</i> and <i>Perkinsiodendron</i>) unresolved. The low resolution of its distal branches and the large number of positively selected genes in the chloroplast genome suggest that the Styracaceae family is in a process of rapid evolution.</p> Conclusions <p>Our research offers novel insights into the evolution of the Styracaceae family and speculates on the molecular mechanisms underlying the family’s adaptive evolution in response to environmental changes.</p>

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Gene loss and positively selected genes in chloroplast genomes reveal adaptive evolution in Styracaceae

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  • 发表日期：

    2026年1月23日

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  • Nai-Wei Li,
  • Chun-Feng Song,
  • Bao-Cheng Wu,
  • Shu-An Wang,
  • Hai-Jun Ma,
  • Xu-Dong Ma,
  • Yi-Gang Song,
  • Jun Wen

摘要

Background

Current research on the Styracaceae family is limited by the number of sampled genera and species, and the comparative analysis of their chloroplast genomes, as well as phylogenetic studies, are quite restricted.

Results

This study conducted a comprehensive comparative analysis of the chloroplast genomes of the Styracaceae family, covering 52 species from 12 genera. Genomic variations occurred mainly among genera but were conserved within each genus. In the specific lineages (Bruinsmia, Alniphyllum, Melliodendron, and Huodendron) of this family, there were cases of fragment insertion or deletion in several genes (accD, clpP, rpoB, rps16, and ycf15), with gene loss or intron loss observed in Bruinsmia (rpoB or rps16, and clpP), Alniphyllum (clpP), and Huodendron (clpP and ycf15). The inverted repeat regions of the genus Melliodendron showed slight contractions. The nucleotide diversity (Pi) of the protein-coding sequences (CDSs) was studied, and six CDSs with Pi values greater than 0.03 were screened out as candidate molecular markers for further phylogenetic research of the family globally. The positive selection analysis indicated that a total of twenty genes were under strong positive selection, while six genes were under weak positive selection. This study determined the phylogeny position of the genus Parastyrax, but leaves the relationships among Clades B (Sinojackia, Pterostyrax, and Halesia carolina), C (Melliodendron and Changiostyrax), and D (Rehderodendron and Perkinsiodendron) unresolved. The low resolution of its distal branches and the large number of positively selected genes in the chloroplast genome suggest that the Styracaceae family is in a process of rapid evolution.

Conclusions

Our research offers novel insights into the evolution of the Styracaceae family and speculates on the molecular mechanisms underlying the family’s adaptive evolution in response to environmental changes.