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

Joung Ho Lee, Jelli Venkatesh, Jinkwan Jo, Siyoung Jang, Geon Woo Kim, Jung Min Kim, Koeun Han, Nayoung Ro, Hea Young Lee, Jin Kyung Kwon, Yong Min Kim, Tae Ho Lee, Doil Choi, Allen Van Deynze, Theresa Hill, Nir Kfir, Aviad Freiman, Nelson H.Davila Olivas, Yonatan Elkind, Ilan Paran*Byoung Cheorl Kang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


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 42 972 gene families in each pepper accession, defining a set of 19 662 core and 23 115 non-core gene families. The new pepper pan-genome includes informative variants, 222 159 PAVs, 12 322 CNVs, and 16 032 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.

Original languageAmerican English
Article numberuhac210
JournalHorticulture Research
StatePublished - 2022
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2022 The Author(s). Published by Oxford University Press on behalf of Nanjing Agricultural University.


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