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אסיף מאגר המחקר החקלאי
פותח על ידי קלירמאש פתרונות בע"מ -
High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers
Year:
2022
Source of publication :
Horticulture Research
Authors :
פארן, אילן
;
.
Volume :
Co-Authors:

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

Facilitators :
From page:
0
To page:
0
(
Total pages:
1
)
Abstract:

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.

Note:
Related Files :
chromosome
Genome
Sweet pepper
עוד תגיות
תוכן קשור
More details
DOI :
10.1093/hr/uhac210
Article number:
0
Affiliations:
Database:
PubMed
Publication Type:
מאמר
;
.
Language:
אנגלית
Editors' remarks:
ID:
62913
Last updated date:
27/12/2022 15:48
Creation date:
27/12/2022 15:48
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Scientific Publication
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

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 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.

Scientific Publication
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