Development of genomic resources for cattails (Typha), a globally important macrophyte genus

Abstract

A critical knowledge gap in freshwater plants research is the lack of genetic resources necessary to answer fundamental questions about their demographic histories, adaptation, and taxonomy. One example of this isTypha, a macrophyte genus essential to wetlands that is also becoming an increasingly problematic biological invader in numerous regions worldwide; while important insights have been discovered for this genus, currently available genetic markers are insufficient to resolve its phylogenetic relationships, population structure, and hybridization dynamics. We performed a cost and time-accessible library preparation for high-throughput sequencing to develop a suite of genomic resources forTypha. Genome-wide nuclear SNPs of 140Typhasamples from North America, temperate Eurasia and Africa revealed three independent genetic clusters corresponding toT. angustifolia,T. domingensisandT. latifolia. Data from ~40% of the nuclear genome was obtained, permitting the characterization of 119,324 nuclear diagnostic markers (SNPs that differentiate the three species). A reference-guided workflow to reconstruct whole-chloroplast-genome sequences was implemented, recovering ~60% of the genome per sample. Three genetic lineages were identified from the cpDNA phylogenetic analysis, agreeing with those determined from nrDNA. With a cost below 15 USD per sample and a processing time of two hours for the library preparation, this is a rapid and cost-effective protocol for population genomic studies. The genomic locations of diagnostic markers and the chloroplast sequences produced in this study will be permanent resources that can be incorporated into future studies ofTypha, a globally important and evolutionarily dynamic genus.