ArticleGenome biology2023
A syntelog-based pan-genome provides insights into rice domestication and de-domestication.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 44 citations in OpenAlex.
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- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- Integrative multi-omics analysis reveals the domestication mechanism of black rice.National science review · 2026Article
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- quota_Anchor: a strand and whole genome duplication-aware collinear gene identification tool.aBIOTECH · 2026Article
- The pangenome enhances the understanding of the genetic diversity of papaya.Horticulture research · 2026Article
- Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution.iScience · 2026Review
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Genetic diversity and evolution of rice centromeres.Nature genetics · 2025Article
- Studies on the mother flower carnation: past, present, and future.Horticulture research · 2025Article
- TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis.Genome biology · 2025Article
- Construction of the graph genomes of Takifugu provides novel insights into the genomic mechanisms of population structure and migratory traits.BMC biology · 2025Article
- A pangenome reference of wild and cultivated rice.Nature · 2025Article
- Genus-Wide Pan-Genome Analysis ofPlants (Basel, Switzerland) · 2025Article
- Integrating Arabidopsis and crop species gene discovery for crop improvement.The Plant cell · 2025Review
- SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.Nucleic acids research · 2025Article
- Telomere-to-telomere, gap-free genome of mung bean (Horticulture research · 2025Article
- The developments and prospects of plant super-pangenomes: Demands, approaches, and applications.Plant communications · 2025Review
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAsian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate.
resultsHere, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice.
conclusionsThis work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.
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