Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

作   者：Xinbo Pang, Hongshan Liu, Suran Wu, Yangchen Yuan, Haijun Li, Junsheng Dong, Zhaohua Liu, Chuanzhi An, Zhihai Su and Bin Li
期刊名称：International Journal of Molecular Sciences
影响因子：4.183
卷 期 号：20(5940)
页     码：1-14
关键词： oak species identification; chloroplast genome; Quercus; mutation hotspots
论文摘要：
Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions(matK-trnK-rps16andtrnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.