School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), School of Life Sciences, Northwest University, Xi'an 710069, China.
Int J Mol Sci. 2018 Jul 5;19(7):1962. doi: 10.3390/ijms19071962.
section is widely distributed across Eurasia at high altitudes, and some species in this section are used as traditional Chinese medicine. Accurate identification of these species is important for their utilization and conservation. Due to similar morphological and chemical characteristics, correct discrimination of these species still remains problematic. Here, we sequenced three complete chloroplast (cp) genomes (, and ). We further compared them with the previously published plastomes from sect. and developed highly polymorphic molecular markers for species authentication. The eight cp genomes shared the highly conserved structure and contained 112 unique genes arranged in the same order, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. We found that four genes (, , and ) were subject to positive selection, and sixteen InDel-variable loci with high discriminatory powers were selected as candidate barcodes. Our phylogenetic analyses based on plastomes further confirmed the monophyly of sect. and primarily elucidated the phylogeny of Gentianales. This study indicated that cp genomes can provide more integrated information for better elucidating the phylogenetic pattern and improving discriminatory power during species authentication.
节在欧亚大陆高海拔地区广泛分布，其中一些物种被用作传统中药。准确识别这些物种对于它们的利用和保护非常重要。由于形态和化学成分相似，正确区分这些物种仍然存在问题。在这里，我们对三个完整的叶绿体 (cp) 基因组 (, 和 ) 进行了测序。我们进一步将它们与以前发表的节叶绿体基因组进行了比较，并开发了用于物种鉴定的高度多态性分子标记。这 8 个 cp 基因组具有高度保守的结构，包含以相同顺序排列的 112 个独特基因，包括 78 个蛋白质编码基因、30 个 tRNA 和 4 个 rRNA。我们分析了这些叶绿体基因组中的重复和核苷酸替换，并检测到几个高度可变的区域。我们发现四个基因 (, , 和 ) 受到正选择的影响，并选择了 16 个具有高鉴别力的 InDel 可变基因座作为候选条形码。我们基于 cp 基因组的系统发育分析进一步证实了节的单系性，并初步阐明了玄参目植物的系统发育。这项研究表明，叶绿体基因组可以为更好地阐明系统发育模式和提高物种鉴定的鉴别能力提供更综合的信息。
