ArticleBMC plant biology2021
Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper.
Article in BMC plant biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Integrated transcriptome-metabolome analyses reveal regulatory networks underlying soluble solids accumulation in Capsicum chinense fruits.The Plant journal : for cell and molecular biology · 2026Article
- Three Novel Genomes Broaden the Wild Side of thePlant direct · 2025Article
- Local gene duplications drive extensive NLR copy number variation across multiple genotypes of Theobroma cacao.G3 (Bethesda, Md.) · 2025Article
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- Genome-wide identification of copy number variation in diverse black pepper accessions.Planta · 2025Article
- Editorial: Exploring structural variants in plant pangenomics: innovations and applications.Frontiers in plant science · 2025Article
- The landscape of sequence variations between resistant and susceptible hot peppers to predict functional candidate genes against bacterial wilt disease.BMC plant biology · 2024Article
- Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis.Nature communications · 2024Article
- A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges.Current research in food science · 2023Review
- Resequencing of durian genomes reveals large genetic variations among different cultivars.Frontiers in plant science · 2023Article
- The Unstable Restorer-of-fertility locus in pepper (Capsicum annuum. L) is delimited to a genomic region containing PPR genes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Whole-genome resequencing reveals genomic footprints of Italian sweet and hot pepper heirlooms giving insight into genes underlying key agronomic and qualitative traits.BMC genomic data · 2022Article
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundPeppers (Capsicum annuum L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper.
resultsHere, we report de novo genome assemblies of Capsicum annuum 'Early Calwonder (non-pungent, ECW)' and 'Small Fruit (pungent, SF)' along with their annotations. In total, we assembled 2.9 Gb of ECW and SF genome sequences, representing over 91% of the estimated genome sizes. Structural and functional annotation of the two pepper genomes generated about 35,000 protein-coding genes each, of which 93% were assigned putative functions. Comparison between newly and publicly available pepper gene annotations revealed both shared and specific gene content. In addition, a comprehensive analysis of nucleotide-binding and leucine-rich repeat (NLR) genes through whole-genome alignment identified five significant regions of NLR copy number variation (CNV). Detailed comparisons of those regions revealed that these CNVs were generated by intra-specific genomic variations that accelerated diversification of NLRs among peppers.
conclusionsOur analyses unveil an evolutionary mechanism responsible for generating CNVs of NLRs among pepper accessions, and provide novel genomic resources for functional genomics and molecular breeding of disease resistance in Capsicum species.
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