Reference quality assembly of the 3.5 Gb genome of Capsicum annuum form a single linked-read library

Authors: Hulse-Kemp, Amanda; MAHESHWARI, SHAMONI - University Of California; STOFFEL, KEVIN - University Of California; HILL, THERESA - University Of California; JAFFE, DAVID - 10x Genomics, Inc; WILLIAMS, STEPHEN - 10x Genomics, Inc; WEISENFELD, NEIL - 10x Genomics, Inc; RAMAKRISHNAN, SRIVIDYA - Johns Hopkins University; KUMAR, VIJAY - 10x Genomics, Inc; SHAH, PREYAS - 10x Genomics, Inc; SCHATZ, MICHAEF - Johns Hopkins University; CHURCH, DEANNA - 10x Genomics, Inc; VAN DEYNZE, ALLEN - University Of California

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/16/2017
Publication Date: 1/12/2018
Publication URL: http://handle.nal.usda.gov/10113/5931558
Citation: Hulse-Kemp, A.M., Maheshwari, S., Stoffel, K., Hill, T.A., Jaffe, D., Williams, S., Weisenfeld, N., Ramakrishnan, S., Kumar, V., Shah, P., Schatz, M.C., Church, D.M., Van Deynze, A. 2018. Reference quality assembly of the 3.5 Gb genome of Capsicum annuum form a single linked-read library. Horticulture Research. 5(4). https://doi: 10.1038/s41438-017-0011-0.
DOI: https://doi.org/10.1038/s41438-017-0011-0

Interpretive Summary: A Clearer Picture of the Genetic Blueprint of Pepper While pepper is not the largest vegetable in the grocery store aisle, the blueprint of what makes pepper a pepper is very complicated compared to other vegetables both in size and number of pieces. There have been three genetic blueprints for pepper developed prior to 2017, however a complete picture has been unable to be generated to date and these are still in many individual pieces because of the difficulties. The lack of a complete genetic outline for pepper limits the utilization of new technologies for breeding a more resilient better tasting pepper. In our experiment we have tested a new technology that provides some additional information about the relationship of individual pieces in the blueprint on the large scale. This enabled us to be able to take some of these current blueprint pieces and join them together correctly to form a blueprint made up of fewer puzzle pieces. For pepper growers and breeders, this means they are able to more accurately know where the puzzle pieces go and use them for targeting pieces of the pepper plant they wish to improve for disease resistance, to increase the size, or even to make the newest hottest pepper. The blueprint constructed here also provides the specific pieces to show the difference between sweet and hot peppers. Additionally the cost of this project is greatly reduced compared to other methods that would have generated similar results. This project will serve as an example of the success that can be generated with this new technology to improve the blueprints for other important crops.

Technical Abstract: Linked-Read sequencing technology has recently been employed successfully for de novo assembly of multiple human genomes, however the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5 gigabase (Gb) diploid pepper (Capsicum annuum) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes for a pungency gene characterized by a large insertion/deletion.