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

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.

Applied Barcoding: The Practicalities of DNA Testing for Herbals

“…These are all factors likely to contribute to lower levels of success in species discrimination in DNA barcoding studies [ 18 ] There is also the possibility of chloroplast capture leading to disparities between nuclear and plastid phylogenetic relationships [ 79 , 80 , 81 , 82 , 83 ]. One way to resolve this would be to sequence the entire plastid genomes of H. perforatum and related species with a view to discovering more effective genetic markers [ 84 , 85 ] or to use the entire plastid genome as a “super-barcode” [ 85 , 86 ].…”

Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species

“…The pan-plastome constructed from multiple accessions per species/variety was expected to facilitate the detection of interspecific variation while avoiding the intraspecific variation that misled the development of non-precise and inapplicable molecular markers. The pan-plastome approach was previously applied to elucidate DNA barcodes for members of the family Zingiberaceae 27 and for diversity assessment and phyloplastomics in the genus Brachypodium 28 . However, the success of the pan-plastome approach is based on the number of fully assembled accessions per species/variety, which in many cases can be very challenging.…”

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

“…Especially, complete chloroplast genome (plastome) sequences provide valuable data sets to resolve complex evolutionary relationships in plastome phylogenies and improve resolution at lower taxonomic levels (e.g., [ 46 , 47 ]). Based on whole plastome alignments, genetic markers for species identification were developed in several studies (e.g., [ 44 , 48 ]).…”