Low-copy nuclear markers in (Isoëtaceae) identified with transcriptomes.

Premise Of The Study: Few genetic markers provide phylogenetic information in closely related species of (Isoëtaceae). We describe the development of primers for several putative low-copy nuclear markers to resolve the phylogeny of , particularly in the southeastern United States.

Methods And Results: We identified regions of interest in transcriptomes based on low-copy genes in other plants. Primers were designed for these regions and tested with 16 taxa of and one species of . Parts of the , , and gene regions show phylogenetic signal within the North American and Mediterranean clades of .

Conclusions: Transcriptome data prove useful for identification and primer design of low-copy genes. Three new markers show potential for inferring phylogenies in regional clades of , and possibly across the entire genus.