Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation

Abstract

Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.

Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis

“…However, the centromeres of Capsicum lacked such satellites but were enriched with Gypsy -LTR, especially CRM retrotransposons. We also found that this pattern was common in C. baccatum , C. chinense and C. pubescens based on recently reported high-quality genomes 11 , although the composition of CRM retrotransposons varied among different Capsicum species. The potato genome also showed the enrichment of CRM in centromeres 21 , but no CRM was identified in the whole genome of P. pruinosa (1.38 Gb, contig N50: 82.2 Mb) 42 , suggesting that Solanaceae centromeres evolved rapidly and were diverse among species.…”

“…Afterward, the quality of several assemblies improved with the development of single-molecule DNA sequencing technologies; for example, the assemblies of cultivar ‘59’ (3.07 Gb, contig N50: 41.27 Mb) 4 , ‘Takanotsume’ (3.05 Gb, contig N50: 99.05 Mb) 5 and CC-090 (3.06 Gb, contig N50: 187.09 Mb) 6 . To date, 23 genome assemblies of cultivated peppers, including C. annuum, C. baccatum , C. chinense , and C. pubescens , are publicly available 7 – 11 , whereas genome sequences for wild peppers are very scarce 7 . Despite continuous improvement, the published assemblies still contain numerous gaps and assembly errors, and complete centromeres and telomeres are missing.…”

A highly sensitive biotin‐based probe for small RNA northern blot and its application in dissecting miRNA function in pepper

“…miRNA targets were predicted using target_detector from SoMART (Li, Orban, et al, 2012). Pepper miRNA targets predicted from zunla2.0 were curated using most recent pepper genome of Zhangshugang (Liu et al, 2023).…”

The genetic architecture of the pepper metabolome provides insights into the regulation of capsianoside biosynthesis

“…Pepper fruit has a broad range of pharmacological applications and is consumed worldwide as a vegetable, fruit, and spice (Srinivasan, 2005; Chen et al, 2009; Meghvansi et al, 2010). Capsicum comprises more than 36 species; however, C. annuum , C. chinense , C. frutescens , C. pubescens , and C. baccatum species have been domesticated over the course of many centuries, and are predominantly cultivated across different pepper-producing regions (Walsh and Hoot, 2001; Carrizo García et al, 2016; Liu et al, 2023). Each species has a distinctive phytochemical and morphological diversity (Antonio et al, 2018; Naves et al, 2022; Liu et al, 2023).…”

“…Capsicum comprises more than 36 species; however, C. annuum , C. chinense , C. frutescens , C. pubescens , and C. baccatum species have been domesticated over the course of many centuries, and are predominantly cultivated across different pepper-producing regions (Walsh and Hoot, 2001; Carrizo García et al, 2016; Liu et al, 2023). Each species has a distinctive phytochemical and morphological diversity (Antonio et al, 2018; Naves et al, 2022; Liu et al, 2023). The most common species, C. annuum , is said to have originated from Mexico and migrated to Africa and Asia via Mesoamerica, and reached Europe ultimately (Hayano-Kanashiro et al, 2016; Tripodi et al, 2021).…”