A New Pepper Genome Built Using Long-Range Short-Read Technology Allows Direct Comparison of Pungent and Non-Pungent Types

The pepper genome is one of the largest in Solanaceae at approximately 3.5 Gigabases and is comprised largely of repetitive elements estimated at 75-80% of the genome. Pepper is a diploid species that has multiple draft genome reference sequences developed using next generation sequencing technology with short reads. However these genomes are largely comprised of a large number of small scaffolds with 37,989 scaffolds in the CM334, 967,017 scaffolds in the Zunla-1, and 1,973,483 scaffolds in the Chiltepin genomes with the largest scaffold N50 at 2.47Mb in the CM334 assembly. Recently third generation technologies have been released that capture long range sequence information in order to enhance the ability of generating higher quality reference sequences with a smaller number of larger scaffolds. These results have been promising on many different species in not only improving existing genomes, but generating new genomes de novo. Ability of breeders and researchers to use the pepper genome for improvement of the crop is dependent on a high-quality reference that provides anchoring and ordering of the majority of the sequence. Thus we have targeted the 10X Genomics Chromium® technology to create a high quality pepper genome, by taking advantage of the long-range information together with affordable short-read technology. 10X Chromium not only builds on scaffolds, but allows for de novo genome assembly in a fraction of the time and cost with little input DNA. Importantly, the resulting assembly is phased as part of the assembly process, allowing for in depth analyses of heterozygous regions and CNVs. Initial results indicate a significant improvement over any pepper short read genome assembly allowing for unprecedented ability for looking into the biology between the differences of pungent and non-pungent peppers.