Development of single‐copy nuclear intron markers for species‐level phylogenetics: Case study with Paullinieae (Sapindaceae)1

Premise of the study: We developed a bioinformatic pipeline that leverages a publicly available genome and published transcriptomes to design primers in conserved coding sequences flanking targeted introns of single‐copy nuclear loci. Paullinieae (Sapindaceae) is used to demonstrate the pipeline. Methods and Results: Transcriptome reads phylogenetically closer to the lineage of interest are aligned to the closest genome. Single‐nucleotide polymorphisms are called, generating a “pseudoreference” closer to the lineage of interest. Several filters are applied to meet the criteria of single‐copy nuclear loci with introns of a desired size. Primers are designed in conserved coding sequences flanking introns. Using this pipeline, we developed nine single‐copy nuclear intron markers for Paullinieae. Conclusions: This pipeline is highly flexible and can be used for any group with available genomic and transcriptomic resources. This pipeline led to the development of nine variable markers for phylogenetic study without generating sequence data de novo.