Representing true plant genomes: haplotype-resolved hybrid pepper genome through trio binning

Authors: DELOREAN, EMILY - National Science Foundation (NSF); YOUNGBLOOD, RAMEY - Mississippi State University; Simpson, Sheron; SCHOONMAKER, ASHLEY - North Carolina State University; Scheffler, Brian; Rutter, William; Hulse-Kemp, Amanda

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/5/2023
Publication Date: 11/16/2023
Citation: Delorean, E.E., Youngblood, R.C., Simpson, S.A., Schoonmaker, A.N., Scheffler, B.E., Rutter, W.B., Hulse-Kemp, A.M. 2023. Representing true plant genomes: haplotype-resolved hybrid pepper genome through trio binning. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2023.1184112.
DOI: https://doi.org/10.3389/fpls.2023.1184112

Interpretive Summary: Obtaining an accurate copy of the true DNA blueprint for the plants that breeders and researchers work with is often very complicated. This is because most of our plants have copies of genetic information that differs from each parent. Historically, these differences have largely been left unresolved or left as a mixed bag in the final representation of our DNA blueprints or genomes. Recent technologies have improved our ability to sequence DNA and software improvements for handling separation of these genetic differences from the parents in an offspring, otherwise known as a trio, mother-father-offspring. We utilized these new resources to show that we could accurately capture the true DNA blueprint for a hybrid pepper plant. We provide a valuable guide on how to apply this technology of trio-binning for other plants.

Technical Abstract: As sequencing costs decrease and availability of high fidelity long-read sequencing increases, generating experiment specific de novo genome assemblies becomes feasible. In many crop species, obtaining the genome of a hybrid or heterozygous individual is necessary for systems that do not tolerate inbreeding or for investigating important biological questions, such as hybrid vigor. However, most genome assembly methods that have been used in plants result in a single sequence representation that is not biologically true of either haplotype within a diploid individual. The resulting genome assembly is often fragmented and exhibits a mosaic or chimera of the two haplotypes, referred to as haplotype-switching. Important haplotype level information, such as causal mutations and structural variation is lost causing difficulties in interpreting downstream analyses. To overcome this challenge, we have applied a method developed for animal genome assembly called trio-binning to an intra-specific hybrid of chili pepper (Capsicum annuum L. cv. HDA149 x Capsicum annuum L. cv. HDA330). We tested all currently available softwares for performing trio-binning, combined with multiple scaffolding technologies including Bionano to determine the optimal method of producing the best haplotype-resolved assembly. Ultimately we produced highly contiguous biologically true haplotype-resolved genome assemblies of the parents, with scaffold N50s of 261.9 Mb and 263.5 Mb, and 99.6% and 99.7% positioned into chromosomes. Overall, the assemblies captured 3.14 Gb and 3.11 Gb of the estimated 3.5 Gb chili pepper genome size. These assemblies represent the complete genome structure of the intraspecific hybrid, as well as the two parental genomes, and show measurable improvements over the currently available reference genomes. Our manuscript provides a valuable guide on how to apply trio-binning to other plant genomes.