Comparative analysis of the complete chloroplast genomes of six white oaks with high ecological amplitude in China

Quercus L. has significant societal, ecological and economic benefits in the Northern Hemisphere. However, species identification among oaks is notoriously difficult. China harbours highly diverse oaks, of which the diversity of white oaks is the most extensive; however, to date, the evolution of chloroplast (cp) genomes in white oaks in China has not been comprehensively studied. Thus, we sequenced the complete cp genomes (161,254 bp, 161,229 bp and 161,254 bp in size) of three white oak species (Quercus serrata Thunb. var. brevipetiolata A. DC. Nakai, Quercus wutaishansea Mary and Quercus mongolica Fischer ex Ledebour, respectively). Six white oak species (Quercus aliena Blume, Quercus dentata Thunb., Quercus aliena Blume var. acutiserrata Maximowicz ex Wenzig, Q. serrata var. brevipetiolata, Q. wutaishanica and Q. mongolica) and five other Fagaceae species (Quercus rubra L., Quercus variabilis Bl., Quercus aquifolioides Rehd. et Wils., Fagus engleriana Seem. and Castanea henryi Skan Rehd. et Wils.) were retrieved for comparative analyses. We detected 11 highly divergent regions (psbA, matK/rps16, rps16, trnS-GCU/trnG-GCC, trnR-UCU/atpA, trnT-GGU/psbD, ndhJ, ndhJ/ndhK, accD, ndhF and ycfI) through comparative analyses and these regions might be used as molecular markers. The ω ratio of the rps12, rpoC2 and ycf1 genes was greater than 1 in several comparison groups between white oaks and the petA gene was subjected to significant positive selection between the comparison of six white oaks and Q. variabilis. Phylogenetic analyses revealed that six white oaks were grouped with Q. rubra, forming a single clade.