Pepper genome sequence and variants

In this database, we provide high-quality reference genomes and annotations of three pepper cultivars, Zhangshugang (belonging to Capsicum annuum var. annuum in the Annuum clade), PI 632928 (C. baccatum var. pendulumC. pubescens in the Pubescens clade). The genome and gene sequences and annotations can be searched, viewed and analyzed using tools implemented in this database.

A graph pan-genome was constructed using the Zhangshugan genome as the reference and structural variants (SVs) identified in PI 632928 and Grif 1614 based on the alignments of their genomes to the Zhangshugan genome. A pepper variome was constructed by sequencing genomes of 500 core Capsicum accessions from C. annuum var. annuum (n = 90), C. annuum var. glabriusculum (n = 22), C. baccatum var. pendulum (n = 109), C. baccatum var. baccatum (n = 9), C. pubescens (n = 38), C. chacoense (n = 17), C. frutescens (n = 99), C. chinense (n = 115) and C. galapagoense (n = 1), and mapping the sequencing reads to the graph pan-genome. A total of about 100 million high-quality SNPs and 7.3 million small indels have been identified and these variants can be explored and analyzed using the 'Variant' module developed in this database.

If you use the data in this database, please cite the following paper:
Liu et al. (2023) Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nature Communications 14:5487