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

Emily E Delorean; Ramey C Youngblood; Sheron A Simpson; Ashley N Schoonmaker; Brian E Scheffler; William B Rutter; Amanda M Hulse-Kemp

doi:10.3389/fpls.2023.1184112

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

Front Plant Sci. 2023 Nov 16:14:1184112. doi: 10.3389/fpls.2023.1184112. eCollection 2023.

Authors

Emily E Delorean^{1

2}, Ramey C Youngblood³, Sheron A Simpson⁴, Ashley N Schoonmaker², Brian E Scheffler⁴, William B Rutter⁵, Amanda M Hulse-Kemp^{1

2}

Affiliations

¹ Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC, United States.
² Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, United States.
³ Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, United States.
⁴ Genomics and Bioinformatics Research Unit, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Stoneville, MS, United States.
⁵ US Vegetable Laboratory, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Charleston, SC, United States.

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 merged single sequence representation that is not a true biologically accurate representation of either haplotype within a diploid individual. The resulting genome assembly is often fragmented and exhibits a mosaic of the two haplotypes, referred to as haplotype-switching. Important haplotype level information, such as causal mutations and structural variation is therefore 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 for each parent, with scaffold N50s of 266.0 Mb and 281.3 Mb, with 99.6% and 99.8% positioned into chromosomes respectively. The assemblies captured 3.10 Gb and 3.12 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.

Keywords: HiFi; genome assembly; haplotype; pepper; trio-binning.

Grants and funding

Support was provided by USDA-ARS research project numbers 6080-22000-031-000D and 6066-21310-005-00-D. This research used resources provided by the SCINet project of the USDA Agricultural Research Service, ARS project number 0500-00093-001-00-D. Support for EED was provided by NSF Postdoctoral Fellowship Award Number: 2010930.