Yang Jia, Vázquez Lucía, Chen Xiaodan, Li Huimin, Zhang Hao, Liu Zhanlin, Zhao Guifang
Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China.
Biology Department, University of Illinois at SpringfieldSpringfield, IL, United States.
Front Plant Sci. 2017 May 19;8:816. doi: 10.3389/fpls.2017.00816. eCollection 2017.
Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and species discrimination of plants. However, the lack of efficient and universal markers often brings particular challenges for genetic studies across different plant groups. In this study, chloroplast genomes from two closely related species ( and ) in Fagaceae were compared to explore universal cpDNA markers for the Chinese oak species in subgenus , a diverse species group without sufficient molecular differentiation. With the comparison, nine and 14 plastid markers were selected as barcoding and phylogeographic candidates for the Chinese oaks. Five (A-H, K-K, 3-S, K, and 1) of the nine plastid candidate barcodes, with the addition of newly designed ITS and a single-copy nuclear gene (SAP), were then tested on 35 Chinese oak species employing four different barcoding approaches (genetic distance-, BLAST-, character-, and tree-based methods). The four methods showed different species identification powers with character-based method performing the best. Of the seven barcodes tested, a barcoding gap was absent in all of them across the Chinese oaks, while ITS and A-H provided the highest species resolution (30.30%) with the character- and BLAST-based methods, respectively. The six-marker combination (A-H + K-K + K + 1 + ITS + SAP) showed the best species resolution (84.85%) using the character-based method for barcoding the Chinese oaks. The barcoding results provided additional implications for taxonomy of the Chinese oaks in subg. , basically identifying three major infrageneric clades of the Chinese oaks (corresponding to Groups , and ) referenced to previous phylogenetic classification of . While the morphology-based allocations proposed for the Chinese oaks in subg. were challenged. A low variation rate of the chloroplast genome, and complex speciation patterns involving incomplete lineage sorting, interspecific hybridization and introgression, possibly have negative impacts on the species assignment and phylogeny of oak species.
叶绿体DNA（cpDNA）常用于植物的物种种群统计学、进化及物种鉴别研究。然而，缺乏高效且通用的标记常常给不同植物类群的遗传学研究带来特殊挑战。在本研究中，对壳斗科两个近缘物种的叶绿体基因组进行比较，以探索用于青冈亚属中国栎类物种的通用cpDNA标记，该类群物种多样但分子分化不足。通过比较，选择了9个和14个质体标记作为中国栎类的条形码和系统地理学候选标记。然后，在35种中国栎类物种上采用四种不同的条形码方法（基于遗传距离、BLAST、特征和树的方法），对9个质体候选条形码中的5个（A-H、K-K、3-S、K和1），加上新设计的ITS和一个单拷贝核基因（SAP）进行了测试。这四种方法显示出不同的物种识别能力，基于特征的方法表现最佳。在测试的7个条形码中，所有中国栎类物种的条形码均未出现条形码间隙，而ITS和A-H分别在基于特征和BLAST的方法中提供了最高的物种分辨率（30.30%）。使用基于特征的条形码方法对中国栎类进行编码时，六标记组合（A-H + K-K + K + 1 + ITS + SAP）显示出最佳的物种分辨率（84.85%）。条形码结果为青冈亚属中国栎类的分类学提供了更多启示，基本确定了中国栎类的三个主要类下分支（对应于组、和），参考了之前的系统发育分类。而基于形态学对青冈亚属中国栎类的分类归属受到了挑战。叶绿体基因组的低变异率，以及涉及不完全谱系分选、种间杂交和基因渗入的复杂物种形成模式，可能对栎类物种的物种归属和系统发育产生负面影响。
