Whole Plastome Sequences from Five Ginger Species Facilitate Marker Development and Define Limits to Barcode Methodology

Plants from the Zingiberaceae family are a key source of spices and herbal medicines. Species identification within this group is critical in the search for known and possibly novel bioactive compounds. To facilitate precise characterization of this group, we have sequenced chloroplast genomes from species representing five major groups within Zingiberaceae. Generally, the structure of these genomes is similar to the basal angiosperm excepting an expansion of 3 kb associated with the inverted repeat A region. Portions of this expansion appear to be shared across the entire Zingiberales order, which includes gingers and bananas. We used whole plastome alignment information to develop DNA barcodes that would maximize the ability to differentiate species within the Zingiberaceae. Our computation pipeline identified regions of high variability that were flanked by highly conserved regions used for primer design. This approach yielded hitherto unexploited regions of variability. These theoretically optimal barcodes were tested on a range of species throughout the family and were found to amplify and differentiate genera and, in some cases, species. Still, though these barcodes were specifically optimized for the Zingiberaceae, our data support the emerging consensus that whole plastome sequences are needed for robust species identification and phylogenetics within this family.

姜科（Zingiberaceae）植物是香料与药用草本的关键来源。对该类群开展物种鉴定，对于发掘已知乃至新型生物活性化合物具有重要意义。为实现对该类群的精准表征，我们对隶属于姜科5个主要类群的物种完成了叶绿体基因组测序。整体而言，这些叶绿体基因组的结构与基部被子植物相似，仅在反向重复A（inverted repeat A, IRA）区域存在3kb的扩增片段。该扩增片段的部分区域在整个姜目（Zingiberales）类群中普遍存在，该类群涵盖姜与香蕉。我们依托全质体基因组比对数据，开发了可最大化区分姜科物种能力的DNA条形码（DNA barcode）。我们的分析流程筛选出了侧翼带有可用于引物设计的高度保守序列的高变异区域。该方法发掘出了此前未被利用的变异区域。这些理论上的最优条形码在该科多个类群的物种中得到验证，可实现属级甚至部分物种级的区分。尽管如此，由于这些条形码专为姜科优化，我们的数据仍支持当前逐渐形成的共识：要实现该类群可靠的物种鉴定与系统发育研究，仍需依赖完整的质体基因组序列。