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. 2017 Sep 30;5(9):apps.1700038.
doi: 10.3732/apps.1700038. eCollection 2017 Sep.

Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci

Maribeth Latvis  1 , Sarah J Jacobs  2   3   4 , Sebastian M E Mortimer  2   3 , Melissa Richards  2 , Paul D Blischak  5 , Sarah Mathews  6 , David C Tank  2   3   4
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Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci

Maribeth Latvis et al. Appl Plant Sci. .

Abstract

Premise of the study: We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility.

Methods and results: We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to take advantage of the Fluidigm microfluidic PCR platform and are well suited for high-throughput sequencing applications. Eighty-seven primers were designed for Castilleja, and 27 were found to have broader utility in Orobanchaceae.

Conclusions: These results demonstrate the utility of these primers, not only across Castilleja, but for other lineages within Orobanchaceae as well. This expanded molecular toolkit will be an asset to future phylogenetic studies in Castilleja and throughout Orobanchaceae.

Keywords: Castilleja; Orobanchaceae; high-throughput sequencing; microfluidic PCR; single-copy nuclear genes.

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Figures

Fig. 1.
Fig. 1.
Relationships among major clades within Orobanchaceae modified from McNeal et al. (2013) with taxa used for primer validation indicated (see text). Bootstrap support values for clades are indicated along the branches and follow McNeal et al. (2013). Reproduced from Latvis et al. (2017a).
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