High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers

Pepper (Capsicum annuum) is an important vegetable crop that has been subjected to intensive breeding, resulting in limited genetic diversity, especially for sweet peppers. Previous studies have reported pepper draft genome assemblies using short read sequencing, but their capture of the extent of large structural variants (SVs), such as presence-absence variants (PAVs), inversions, and copy-number variants (CNVs) in the complex pepper genome falls short. In this study, we sequenced the genomes of representative sweet and hot pepper accessions by long-read and/or linked-read methods and advanced scaffolding technologies. First, we developed a high-quality reference genome for the sweet pepper cultivar 'Dempsey' and then used the reference genome to identify SVs in 11 other pepper accessions and constructed a graph-based pan-genome for pepper. We annotated an average of 42972 gene families in each pepper accession, defining a set of 19662 core and 23115 non-core gene families. The new pepper pan-genome includes informative variants, 222159 PAVs, 12322 CNVs, and 16032 inversions. Pan-genome analysis revealed PAVs associated with important agricultural traits, including potyvirus resistance, fruit color, pungency, and pepper fruit orientation. Comparatively, a large number of genes are affected by PAVs, which is positively correlated with the high frequency of transposable elements (TEs), indicating TEs play a key role in shaping the genomic landscape of peppers. The datasets presented herein provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement.

Automated summary

In this study, the genomes of representative sweet and hot pepper accessions were sequenced using long-read and/or linked-read methods. A high-quality reference genome was developed for the sweet pepper cultivar 'Dempsey' and used to identify structural variants in other pepper accessions. The pan-genome analysis revealed important agricultural traits associated with presence-absence variants and highlighted the role of transposable elements in shaping the genomic landscape of peppers.