title: Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes.
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.
authors: INRA/UBP UMR 1095 GDEC (Génétique, Diversité et Ecophysiologie des Céréales), Clermont Ferrand, France.
authors: Florent
authors: F
authors: Murat
authors: Rongzhi
authors: R
authors: Zhang
authors: Sébastien
authors: S
authors: Guizard
authors: Raphael
authors: R
authors: Flores
authors: Alix
authors: A
authors: Armero
authors: Caroline
authors: C
authors: Pont
authors: Delphine
authors: D
authors: Steinbach
authors: Hadi
authors: H
authors: Quesneville
authors: Richard
authors: R
authors: Cooke
authors: Jerome
authors: J
authors: Salse
mesh_terms: D032461:Chromosomes, Plant; D019143:Evolution, Molecular; D017353:Gene Deletion; D020440:Gene Duplication; D005799:Genes, Dominant; D017343:Genes, Plant; D023281:Genomics / Q000379:methods; D059785:Karyotype; D010802:Phylogeny; D006109:Poaceae / Q000235:genetics*; D011123:Polyploidy; D011995:Recombination, Genetic; D012984:Software
keywords: ancestor; dominance; duplication; evolution; genome; synteny