Building a model: Developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

Milkweeds (Asclepias L.: Apocynaceae) are important models for the evolutionary ecology of plant reproduction, plant hybridization, plant defense and plant-herbivore co-evolution. To facilitate further advances in these areas, as well as open new avenues of research, we have initiated a project to sequence the 835 Mbp genome of common milkweed (A. syriaca L.), a widespread and intensively studied species, to a minimum of 25X coverage using Illumina sequencing technology. With a lower coverage preliminary data set, we have assembled most of the high copy fractions and some of the low-copy fraction of the common milkweed genome using a combination of reference guided and de novo assembly strategies. A complete 155 kbp plastome sequence, more than 400 kbp of mitochondrial genome sequence, and a 7.5 kbp nuclear ribosomal DNA cistron were assembled and characterized. Low-copy nuclear genes were assembled through a comparative genomics approach utilizing data from other asterids. The repeats present in the milkweed genome were surveyed, and from among these microsatellite loci were identified and evaluated. The markers obtained through this sequencing effort will be applied to milkweed genetic map development and to estimate phylogenetic relationships among the 135 species of Asclepias. This project will provide the first insights into the genomic basis of the incredible morphological and ecological diversity observed among milkweeds. The genome will also serve as a community resource for studies of plant-herbivore and plant-pollinator co-evolution, floral developmental genetics, chemical evolution, population genetics, and comparative genomics.