文献类型：期刊文献

英文题名：Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

作者：Pang, Xinbo[1,2,3,4] Liu, Hongshan[2] Wu, Suran[2] Yuan, Yangchen[2] Li, Haijun[2] Dong, Junsheng[2] Liu, Zhaohua[2] An, Chuanzhi[2] Su, Zhihai[2] Li, Bin[1,2,3,4]

第一作者：Pang, Xinbo

通信作者：Li, B[1];Li, B[2];Li, B[3];Li, B[4]

机构：[1]Chinese Acad Forestry, Res Inst Forestry, Beijing 100091, Peoples R China;[2]Adm Bur Hongyashan State Owned Forest Farm Yixian, Yixian 074200, Peoples R China;[3]Chinese Acad Forestry, State Key Lab Tree Genet & Breeding, Beijing 100091, Peoples R China;[4]Chinese Acad Forestry, State Forestry Adm, Key Lab Tree Breeding & Cultivat, Beijing 100091, Peoples R China

年份：2019

卷号：20

期号：23

外文期刊名：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

收录：;Scopus(收录号：2-s2.0-85075512874);WOS:【SCI-EXPANDED(收录号:WOS:000504428300122)】；

基金：The study was funded by by "national forest germplasm resources bank of Quercus mongolica and Quercus variabilis in Hongyashan of Hebei (2017, 2018, 2019)".

语种：英文

外文关键词：oak species identification; chloroplast genome; Quercus; mutation hotspots

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-rps16 and trnR-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.