利用叶绿体基因组大单拷贝区的单核苷酸多态位点鉴定紫薇属和马尾藻属植物

A Novel Method for Identification of Lagerstroemia and Sargassum Taxa Using Single Nucleotide Polymorphic Characters from the Large Single-Copy Region of Complete Chloroplast Genomes

摘要: 由于植物的种间和属间存在或多或少的形态相似性，用于植物分类的有价值的形态性状数量有限。DNA短片段提供的信息量少，只能区分有限数量的植物种。精确鉴定和数字化管理全球植物，仍然是极其具有挑战性的难题。本文报道，在一个核苷酸分子水平上精确鉴定紫薇属植物的新方法。叶绿体基因组的大单拷贝区的单核苷酸多态位点，作为关键的分子性状用于编制分子分类检索表。为了达到简化和精确鉴定的目的，回避使用如下3类基因组DNA区域的分子性状，即gap区域、poly结构区域及简单重复序列区域。本研究对于紫薇属植物的分类修订、数字化管理、保护和利用具有重要价值。海洋植物大型藻类马尾藻科马尾藻属的9个种/变种也可以用同样的方法成功鉴定，表明我们的方法不仅适用于高等植物的鉴定，也适用于低等植物藻类。

Abstract: Morphological features to some extent are similar among plant species/genera, so the number of distinguishable morphological traits useful for plant taxonomy is limited. With the progress of global projects of the tree of life, 4 universal DNA barcodes (rbcL, matK, trnH-psbA and ITS) are recommended for global plant classification, 3 (rbcL, matK, and trnH-psbA) of which are from the chloroplast (cp) genome. However, short DNA fragments provide less information and relatively limited number of plant species can be resolved satisfactorily. Assembling and operating the complete cp genome with approximate 150 kb in length require skilled high-level experts and involve a large workload. It is still difficult to accurately identify and digitally manage the global plants. To provide a more convenient, simple and accurate method for plant identification and classification, for the first time, we used single-nucleotide polymorphic characters from the large single-copy (LSC) region of the cp genome for compilation of molecular taxonomic keys to Lagerstroemia species. To ensure simplification and accurate identification, we avoided the use of molecular traits from the following three categories of genomic DNA regions: gap regions, poly-N regions and simple sequence repeat regions. With the huge number of plant species in the world, genetic variations, such as those resulted from gene transfer and loss, may cause the target DNA region to be unavailable and further make comparative analysis impossible in plant DNA barcoding in some cases, but the LSC region is present in each cp genome in the plant kingdom. Thus, comparative analysis of all plant species worldwide can be conducted based on sequences from the LSC region. The cp genome can provide rich information for plant identification. Our new methodology is valuable for improving plant taxonomic revision, upgrading the digital management platform and accelerating phylogenetic and phytogeographic insights into global plants. Nine Sargassum species/varieties (Sargassaceae) of marine plants were also successfully identified in the similar way, indicating that our method is suitable not only for identification and classification of higher plants, but also algae of lower plants.