Structural conservation and functional genetic adaptive evolution of chloroplast genomes in Cycle-cup Oaks

Abstract

Abstract Background: Cycle-cup oaks (Quercus section Cyclobalanopsis) 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 course, tempo, and mode of genome evolution in cycle-cup oaks remain largely unknown; in particular, how plant plastome genes and genomes evolve during rapid speciation. To address this question, we analyzed the complete plastomes of 50 species of Quercus section Cyclobalanopsis, 36 newly sequenced and 14 published species. Results: Based on a series of analyses, including genome structure, genome annotation, GC content, repeat sequences, SSR components, codon usage bias, and comparative genomics, we found that Quercus section Cyclobalanopsishad a conserved plastome structure. Highly divergent regions, such as the ndhFand ycf1 gene regions and the petN—psbM and rpoB—trnC-GCA gene spacer regions, provided potential molecular markers for subsequent analysis. The maximum likelihood phylogenetic tree based on complete chloroplast genomes, coding DNA sequences, and highly divergent regions produced a poorly resolved genetic relationship of the plastid lineages of section Cyclobalanopsis. We identified nine protein-coding genes containing sites for positive selection: ndhA, ndhD, ndhF, ndhH, rbcL, rpl32, accD, ycf1, and ycf2. Conclusions: We compared and analyzed the chloroplast genomes of 50 species of Quercus section Cyclobalanopsis to explore their diversity structure, phylogenetic relationships, and ecological adaptative evolution. These chloroplast genome data provide valuable information for deep insights into phylogenetic relationships and intraspecific diversity in Quercus.