Abstract
Premise of the StudyFew genetic markers provide phylogenetic information in closely related species of Isoëtes (Isoëtaceae). We describe the development of primers for several putative low‐copy nuclear markers to resolve the phylogeny of Isoëtes, particularly in the southeastern United States.Methods and ResultsWe identified regions of interest in Isoëtes transcriptomes based on low‐copy genes in other plants. Primers were designed for these regions and tested with 16 taxa of Isoëtes and one species of Lycopodium. Parts of the pgiC, gapC, and IBR3 gene regions show phylogenetic signal within the North American and Mediterranean clades of Isoëtes.ConclusionsTranscriptome data prove useful for identification and primer design of low‐copy genes. Three new markers show potential for inferring phylogenies in regional clades of Isoëtes, and possibly across the entire genus.
Highlights
METHODS AND RESULTSWe identified regions of interest in Isoëtes transcriptomes based on low-copy genes in other plants
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Parts of the pgiC, gapC, and IBR3 gene regions show phylogenetic signal within the North American and Mediterranean clades of Isoëtes
Summary
Markers of interest were selected based on a literature search of reportedly low-copy nuclear markers in ferns and mosses (Table 1; Szövényi et al, 2006; Schuettpelz et al, 2008; Rothfels et al, 2013). Nucleotide sequences for these markers were obtained from the National Center for Biotechnology Information’s (NCBI) GenBank (http://www.ncbi.nlm.nih.gov/genbank/; Clark et al, 2016) or TreeBASE (http://www.treebase.org; Sanderson et al, 1994) databases. Using the BLAST+ 2.4 software package (Camacho et al, 2009), local BLAST databases were constructed from each Isoëtes transcriptome. PgiC IBR3_1 IBR3_2 Transducin_1 Transducin_2 gapC_short gapC_long pgiC_1156F pgiC_1900R IBR3_2F IBR3_6R IBR3_13F IBR3_16R Transducin_1F Transducin_1R Transducin_2F Transducin_2R gapC_5F gapC_7R gapC_5F gapC_9R
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