New insights on the phylogeny, evolutionary history, and ecological adaptation mechanism in cycle‐cup oaks based on chloroplast genomes

Cycle-cup oaks (<i>Quercus</i> section <i>Cyclobalanopsis</i>) are one of the principal components of forests in the tropical and subtropical climates of East and Southeast Asia. They have experienced relatively recent increases in the diversification rate, driven by changing climates and the Himalayan orogeny. However, the evolutionary history and adaptive mechanisms at the chloroplast genome level in cycle-cup oaks remain largely unknown. Therefore, we studied this problem by conducting chloroplast genomics on 50 of the ca. 90 species. Comparative genomics and other analyses showed that <i>Quercus</i> section <i>Cyclobalanopsis</i> had a highly conserved chloroplast genome structure. Highly divergent regions, such as the <i>ndhF</i> and <i>ycf1</i> gene regions and the <i>petN</i>-<i>psbM</i> and <i>rpoB-trnC-GCA</i> intergenic spacer regions, provided potential molecular markers for subsequent analysis. The chloroplast phylogenomic tree indicated that <i>Quercus</i> section <i>Cyclobalanopsis</i> was not monophyletic, which mixed with the other two sections of subgenus <i>Cerris</i>. The reconstruction of ancestral aera inferred that Palaeotropics was the most likely ancestral range of <i>Quercus</i> section <i>Cyclobalanopsis</i>, and then dispersed to Sino-Japan and Sino-Himalaya. Positive selection analysis showed that the photosystem genes had the lowest <i>ω</i> values among the seven functional gene groups. And nine protein-coding genes containing sites for positive selection: <i>ndhA</i>, <i>ndhD</i>, <i>ndhF</i>, <i>ndhH</i>, <i>rbcL</i>, <i>rpl32</i>, <i>accD</i>, <i>ycf1</i>, and <i>ycf2</i>. This series of analyses together revealed the phylogeny, evolutionary history, and ecological adaptation mechanism of the chloroplast genome of <i>Quercus</i> section <i>Cyclobalanopsis</i> in the long river of earth history. These chloroplast genome data provide valuable information for deep insights into phylogenetic relationships and intraspecific diversity in <i>Quercus</i>.