Targeted Sequencing of Genes and Transcripts from Soybean and Wheat using NimbleGen SeqCap EZ and PacBio SMRT Sequencing

Full-length gene capture solutions offer opportunities to screen and characterize structural variations and genetic diversity to understand key traits in plants and animals. Through a combined Roche NimbleGen probe capture and SMRT Sequencing strategy, we demonstrate the capability to resolve complex gene structures often observed in plant defense genes and developmental genes spanning multiple kilobases. The custom panel includes members of the WRKY plant-defense-signaling family,  members of the NB-LRR disease-resistance family, and developmental genes important for flowering.  The presence of repetitive structures and low-complexity regions makes short-read sequencing of these genes difficult, yet this approach allows researchers to obtain complete sequences for unambiguous resolution of both gene models and transcript isoforms.  This strategy has been applied to both genomic DNA and RNA samples from soybean and wheat coupled with barcoding for multiplexing.