Abstract
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.
Highlights
The Zingiberaceae family includes ginger, turmeric, and cardamom spices, as well as many species with medicinal applications [1]
And annotation We performed de novo assembly on the Z. officinale chloroplast genome using DNA sequences from a shotgun library of total cell DNA
Though the ginger-specific barcodes reported in this study, JNV-C and JNV-A, have at least 5 polymorphisms between these two species, they too are ineffective with regard to Curcuma species (Figure 3B–C), suggesting far fewer polymorphisms exist across plastomes of that genus
Summary
The Zingiberaceae family includes ginger, turmeric, and cardamom spices, as well as many species with medicinal applications [1]. These plants have received little characterization at the genome level, there are many justifications for initiating such studies. Previous work on the phylogenetic characterization of Zingiberaceae has focused on a small number of shared loci. While these loci can be used to differentiate genera, the approach fails to resolve genera into species [3]. Even for deeper phylogentic relationships, the Zingiberaceae contain many discrepancies between morphological and molecular classification of species; genera such as the Alpinia [4] and, to a lesser extent, Curcuma [3] are apparently paraphyletic
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