ArticleGenome biology and evolution2014
Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
- Comparative genomics approach to infer ancestral cell karyotypes and reconstruct the evolutionary trajectories of plant chromosomes.Nature protocols · 2025Review
- Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution, lignin biosynthesis regulation, and stress tolerance.Science China. Life sciences · 2024Article
- Genome-Wide Identification and Expression Analysis of Catalase Gene Families inPlants (Basel, Switzerland) · 2023Article
- The lack of negative association between TE load and subgenome dominance in synthesizedProceedings of the National Academy of Sciences of the United States of America · 2023Article
- SyntenyViewer: a comparative genomics-driven translational research tool.Database : the journal of biological databases and curation · 2023Article
- The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits.Plant communications · 2023Article
- Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae.Genome biology and evolution · 2023Article
- A common whole-genome paleotetraploidization in Cucurbitales.Plant physiology · 2022Article
- The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation.The Plant cell · 2022Article
- Subgenome dominance and its evolutionary implications in crop domestication and breeding.Horticulture research · 2022Article
- Karyotype Reorganization in Wheat-Rye Hybrids Obtained via Unreduced Gametes: Is There a Limit to the Chromosome Number in Triticale?Plants (Basel, Switzerland) · 2021Article
- Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence.BMC genomics · 2021Article
- Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae).Frontiers in plant science · 2021Article
- Asymmetric Divergence in Transmitted SNPs of DNA Replication/Transcription and Their Impact on Gene Expression in PolyploidFrontiers in genetics · 2021Article
- Chromosome Pairing in Polyploid Grasses.Frontiers in plant science · 2020Review
- Illegitimate Recombination Between Homeologous Genes in Wheat Genome.Frontiers in plant science · 2020Article
- Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution.Genes · 2019Article
- Reconstruction of evolutionary trajectories of chromosomes unraveled independent genomic repatterning between Triticeae and Brachypodium.BMC genomics · 2019Article
- Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA.Genome biology · 2019Article
- Recursive Paleohexaploidization Shaped the Durian Genome.Plant physiology · 2019Article
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10 authors.
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Abstract
Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted, and shuffled, defining dominant (bias toward duplicate retention) and sensitive (bias toward duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in seven protochromosomes containing 16,464 protogenes and following evolutionary rules where 1) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) subgenomes, 2) subgenome dominance is revealed by both gene deletion and shuffling from the S blocks, 3) duplicate deletion/movement may have been mediated by single-/double-stranded illegitimate recombination mechanisms, 4) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, 5) the fusion of two dominant blocks leads to supradominant neochromosomes (D + D = D) with higher ancestral gene retention compared with D + S = D (i.e., fusion of blocks with opposite sensitivity) or even S + S = S (i.e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named "PlantSyntenyViewer," available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data.
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