title: Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps.
abstract: Large-scale (segmental or whole) genome duplication has been recurring in angiosperm evolution. Subsequent gene loss and rearrangements further affect gene copy numbers and fractionate ancestral gene linkages across multiple chromosomes. The fragmented "multiple-to-multiple" correspondences resulting from this distinguishing feature of angiosperm evolution complicates comparative genomic studies. Using a robust computational framework that combines information from multiple orthologous and duplicated regions to construct local syntenic networks, we show that a shared ancient hexaploidy event (or perhaps two roughly concurrent genome fusions) can be inferred based on the sequences from several divergent plant genomes. This "paleo-hexaploidy" clearly preceded the rosid-asterid split, but it remains equivocal whether it also affected monocots. The model resulting from our multi-alignments lays the foundation for approximating the number and arrangement of genes in the last universal common ancestor of angiosperms. Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes.
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
authors.forename: John E
authors.initials: JE
authors.lastname: Bowers
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
authors.forename: Maqsudul
authors.initials: M
authors.lastname: Alam
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D016000:Cluster Analysis; D019143:Evolution, Molecular; D020440:Gene Duplication; D023061:Gene Order; D017343:Genes, Plant; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics*; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D011123:Polyploidy; D026801:Synteny