The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Bejing 100700, China.
Molecules. 2018 Dec 20;24(1):15. doi: 10.3390/molecules24010015.
Herb genomics and comparative genomics provide a global platform to explore the genetics and biology of herbs at the genome level. C.A. Meyer is an important medicinal plant for a variety of bioactive chemical compounds of which the biosynthesis may involve transport of a wide range of substrates mediated by oligopeptide transporters (OPT). However, information about the OPT family in the plant kingdom is still limited. Only 17 and 18 OPT genes have been characterized for and , respectively. Additionally, few comprehensive studies incorporating the phylogeny, gene structure, paralogs evolution, expression profiling, and co-expression network between transcription factors and OPT genes have been reported for ginseng and other species. In the present study, we performed those analyses comprehensively with both online tools and standalone tools. As a result, we identified a total of 268 non-redundant OPT genes from 12 flowering plants of which 37 were from ginseng. These OPT genes were clustered into two distinct clades in which clade-specific motif compositions were considerably conservative. The distribution of OPT paralogs was indicative of segmental duplication and subsequent structural variation. Expression patterns based on two sources of RNA-Sequence datasets suggested that some OPT genes were expressed in both an organ-specific and tissue-specific manner and might be involved in the functional development of plants. Further co-expression analysis of OPT genes and transcription factors indicated 141 positive and 11 negative links, which shows potent regulators for OPT genes. Overall, the data obtained from our study contribute to a better understanding of the complexity of the OPT gene family in ginseng and other flowering plants. This genetic resource will help improve the interpretation on mechanisms of metabolism transportation and signal transduction during plant development for .
草药基因组学和比较基因组学为在基因组水平上探索草药的遗传学和生物学提供了一个全球化的平台。C.A. Meyer 是一种重要的药用植物，其多种生物活性化合物的生物合成可能涉及到由寡肽转运体（OPT）介导的广泛底物的运输。然而，关于植物王国中 OPT 家族的信息仍然有限。仅对 和 分别鉴定了 17 个和 18 个 OPT 基因。此外，对于人参和其他物种，很少有综合研究将 OPT 基因与转录因子的系统发育、基因结构、旁系同源进化、表达谱和共表达网络结合起来。在本研究中，我们使用在线工具和独立工具全面进行了这些分析。结果，我们从 12 种开花植物中总共鉴定出 268 个非冗余 OPT 基因，其中 37 个来自人参。这些 OPT 基因被聚类为两个不同的分支，其中分支特异性基序组成相当保守。OPT 旁系同源物的分布表明发生了片段复制和随后的结构变异。基于两个 RNA-Seq 数据集的表达模式表明，一些 OPT 基因以器官特异性和组织特异性方式表达，可能参与植物的功能发育。进一步对 OPT 基因和转录因子的共表达分析表明，有 141 个正相关和 11 个负相关链接，这表明 OPT 基因有强大的调控因子。总的来说，我们的研究数据有助于更好地理解人参和其他开花植物中 OPT 基因家族的复杂性。这些遗传资源将有助于提高对植物发育过程中代谢运输和信号转导机制的解释。
