| Summary: | Plant chloroplast (cp) gene clusters consist of genes arranged closely together on the cp genome. These genes are organized in operon structures and participate in cotranscription, typically exhibiting conservation. Broken gene clusters have been observed in gymnosperms. In order to investigate whether the substitution rates and selection pressure of associated genes are affected following the disruption of gene clusters, the cp genomes of 80 species (78 gymnosperms and 2 outgroups) were analyzed. A phylogenetic analysis was conducted using 58 shared genes to examine the evolutionary rates and selection pressure of genes associated with gene clusters and protein-coding genes in <i>Sciadopitys verticillata</i>. The results demonstrate that <i>S. verticillata</i> exhibited the highest number of rearrangements compared to the <i>Cycas revoluta</i> genome. Four gene clusters (<i>rps2</i>, <i>psbB</i>, <i>rpoB</i>, and <i>petL</i> clusters) in <i>S. verticillata</i> were disrupted, while <i>rps2</i> in <i>Callitris rhomboidea</i> experienced disruption. Significantly increased evolutionary rates were observed in 12 out of 18 gene cluster-related genes in <i>S. verticillata</i>. Following disruption, <i>S. verticillata</i> and <i>C. rhomboidea</i> exhibited an increase in gene cluster-related genes, particularly <i>rps2</i>, and higher selection pressure on both <i>rps2</i> and <i>atpA</i> genes compared to other species. Furthermore, among the 58 genes shared by <i>S. verticillata</i>, the evolutionary rates of 36 genes increased, and the selection pressure on 13 genes exceeded that of other species. These results indicate an increased substitution rate of gene clusters in <i>S. verticillata</i> and <i>C. rhomboidea</i>. The large-scale rearrangement and elevated substitution rates of the cp genome in <i>S. verticillata</i> were revealed. This study sheds light on the heterogeneity of cp genome evolution in gymnosperms.
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