Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

  1. Haibao Tang1,2,
  2. Xiyin Wang1,3,
  3. John E. Bowers1,
  4. Ray Ming4,
  5. Maqsudul Alam5, and
  6. Andrew H. Paterson1,2,6
  1. 1 Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA;
  2. 2 Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA;
  3. 3 College of Science, Hebei Polytechnic University, Tangshan, Hebei 063000, China;
  4. 4 Department of Plant Biology, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, USA;
  5. 5 Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA

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.

Footnotes

  • 6 Corresponding author.

    6 E-mail paterson{at}uga.edu; fax (706) 583-0160.

  • [Supplemental material is available online at www.genome.org.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.080978.108.

    • Received May 15, 2008.
    • Accepted September 2, 2008.

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