Premise of the study: Chloroplast primers were developed from genomic data for the taxonomically challenging genus Castilleja. We further tested the broader utility of these primers across Orobanchaceae, identifying a core set of chloroplast primers amplifying across the clade. Methods and Results: Using a combination of three low-coverage Castilleja genomes and sequence data from 12 Castilleja plastomes, 76 primer combinations were specifically designed and tested for Castilleja. The primers targeted the most variable portions of the plastome and were validated for their applicability across the clade. Of these, 38 primer combinations were subsequently evaluated in silico and then validated across other major clades in Orobanchaceae. Conclusions: These results demonstrate the utility of these primers, not only across Castilleja, but for other clades in Orobanchaceae-particularly hemiparasitic lineages-and will contribute to future phylogenetic studies of this important clade of parasitic plants. .
Bibliographical noteFunding Information:
1Manuscript received 27 February 2017; revision accepted 10 April 2017. This research was supported by resources at the Institute for Bioinfor-matics and Evolutionary Studies (IBEST; NIH/NCRR P20RR16448 and P20RR016454) and by the following awards from the National Science Foundation: DEB-1253463 (awarded to D.C.T.), DEB-1502061 (awarded to D.C.T. for S.J.J.), and DEB-1210895 (awarded to D.C.T. for S.U.C.). 8Author for correspondence: Maribeth.Latvis@sdstate.edu †Deceased 21 May 2017.
- high-throughput sequencing
- microfluidic PCR