ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2023
Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2023. 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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12 citing papers in PubMed, 19 citations in OpenAlex.
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- Three Novel Genomes Broaden the Wild Side of thePlant direct · 2025Article
- The gap-free assembly of pepper genome reveals transposable-element-driven expansion and rapid evolution of pericentromeres.Plant communications · 2025Article
- Phenotypic simulation for fruit-related traits in FMolecular genetics and genomics : MGG · 2025Article
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- Identification of inheritance and genetic loci responsible for wrinkled fruit surface phenotype in chili pepper (Molecular breeding : new strategies in plant improvement · 2025Article
- Genome-Wide Identification and Characterization of SNPs and InDels ofPlants (Basel, Switzerland) · 2024Article
- Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis.Nature communications · 2024Article
- Chili pepper extracts, capsaicin, and dihydrocapsaicin as potential anticancer agents targeting topoisomerases.BMC complementary medicine and therapies · 2024Article
- Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family.Frontiers in plant science · 2024Review
- Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning.Frontiers in plant science · 2023Article
- Current status, breeding strategies and future prospects for managing chilli leaf curl virus disease and associated begomoviruses in Chilli (Frontiers in plant science · 2023Review
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Authors and funding
5 authors at 4 institutions in 1 country.
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Abstract
Here, we report the genome sequence of a popular Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'. We used long-read sequencing and optical mapping, together with the genetic mapping technique, to obtain the chromosome-scale genome assembly of 'Takanotsume'. The assembly consists of 12 pseudomolecules, which corresponds to the basic chromosome number of C. annuum, and is 3,058.5 Mb in size, spanning 97.0% of the estimated genome size. A total of 34,324 high-confidence genes were predicted in the genome, and 83.4% of the genome assembly was occupied by repetitive sequences. Comparative genomics of linked-read sequencing-derived de novo genome assemblies of two Capsicum chinense lines and whole-genome resequencing analysis of Capsicum species revealed not only nucleotide sequence variations but also genome structure variations (i.e. chromosomal rearrangements and transposon-insertion polymorphisms) between 'Takanotsume' and its relatives. Overall, the genome sequence data generated in this study will accelerate the pan-genomics and breeding of Capsicum, and facilitate the dissection of genetic mechanisms underlying the agronomically important traits of 'Takanotsume'.
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