Primers for Castilleja and their utility across Orobanchaceae: II. Single‐copy nuclear loci¹

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.

Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR‐based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics

“…Moreover, allelic information from nuclear loci, which is essential for the study of plant groups where allopolyploidy may be common, can be obtained directly from the pool of PCR products without the necessity of cloning (e.g., Blischak et al., ). These approaches, including primers designed for specific focal taxa (e.g., genus level), have been shown to work across entire families (e.g., Latvis et al., , b) and orders (e.g., Collins et al., ).…”

Phylogenetic Relationships in Orobanchaceae Inferred From Low-Copy Nuclear Genes: Consolidation of Major Clades and Identification of a Novel Position of the Non-photosynthetic Orobanche Clade Sister to All Other Parasitic Orobanchaceae

“…A number of nuclear genes have recently been used to improve molecular phylogenetic analyses in plants. These include low-copy nuclear (LCN) Conserved Ortholog Set (COS) genes (Sang, 2002; Li M. et al, 2008; Duarte et al, 2010; Zhang et al, 2012; Zimmer and Wen, 2012, 2015; Babineau et al, 2013; Latvis et al, 2017) as well as multi-gene families, most notably pentatricopeptide repeat (PPR) genes (Yuan et al, 2009, 2010; Crowl et al, 2014). Members of the PPR protein family are sequence-specific RNA-binding proteins functioning in gene expression of chloroplasts and mitochondria (O’Toole et al, 2008; Barkan and Small, 2014), with over 400 members in the genomes of most plants sampled thus far (Yuan et al, 2010).…”

“…Screening the model plants rice ( Oryza sativa ) and Arabidopsis thaliana , Yuan et al (2010) found 127 PPR genes to be single copy, of which five were used to resolve phylogenetic relationships in selected Verbenaceae (Yuan et al, 2010). The applicability of LCN genes may decrease at deeper phylogenetic depth (e.g., of 274 LCN loci screened in Fabaceae by Choi et al, 2006, only ten markers were suitable at the family level), which may explain why beyond phytochrome genes (PHYA and PHYB) no LCN locus has been applied across the entire Orobanchaceae (but see Latvis et al, 2017, for a list of primers from a number of single-copy nuclear loci).…”