De Novo Assembly of an Ornamental Plant Genome - Penstemon barbatus

Penstemon is one of the most attractive ornamental plants in North America. A Penstemon reference genome would facilitate the development of novel cultivars with improved ornamental traits, disease resistance, and drought resistance. Penstemon is also a model plant for studying the evolution of pollination syndromes. Some Penstemon species are pollinated by bees, while others are pollinated by hummingbirds. The Penstemon barbatus genome will be used as a template genome to investigate evolution of pollination syndrome diversity. Generating de novo reference genome assemblies for large plant genome usually requires great effort and a large amount of data from several sequencing platforms. Furthermore, repetitive regions in plant genomes are always an obstacle for precise genome assembly. By using PacBio sequence data and Bionano optical mapping techniques, we present a de novo, high quality reference assembly for Penstemon barbatus, a hummingbird-pollinated species, which demonstrates the usefulness of a long-read sequencing approach to efficiently create new reference assemblies for dicotyledon species. The Penstemon reference genome (1C=750 Mb) was created using 7 million PacBio RS II P6-C4 reads generated from 45 SMRT cells, at a total cost of $14,772 (including library prep). PacBio raw reads were corrected, trimmed and assembled by using the Canu 1.3 pipeline on 512Gb RAM high memory cluster. We generated 5,902 contigs using this method with a contig N50 size of 1.06 megabases. (update data soon) The high quality of this genome assembly illustrates how this methodology can be used to efficiently generate new dicotyledons reference genome assemblies at reasonably low cost without requiring data from multiple sequencing platforms. Using this genome as a reference, we are in the process of assembling the genome of the closely related, bee-pollinated species P. neomexicanus, using a single Illumina HiSeq 400 150bp paired-end lane (approximately 130 X coverage for $2,450, including library preparation).