title: A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.
abstract: BACKGROUND
  Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.
  
  
  RESULTS
  Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.
  
  
  CONCLUSIONS
  When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.
authors: Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA.
authors: Andrea
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authors: Zuccolo
authors: John E
authors: JE
authors: Bowers
authors: James C
authors: JC
authors: Estill
authors: Zhiyong
authors: Z
authors: Xiong
authors: Meizhong
authors: M
authors: Luo
authors: Aswathy
authors: A
authors: Sebastian
authors: José Luis
authors: JL
authors: Goicoechea
authors: Kristi
authors: K
authors: Collura
authors: Yeisoo
authors: Y
authors: Yu
authors: Yuannian
authors: Y
authors: Jiao
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authors: Duarte
authors: Haibao
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authors: Tang
authors: Saravanaraj
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authors: Ayyampalayam
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authors: Rounsley
authors: Dave
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authors: Kudrna
authors: Andrew H
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authors: Paterson
authors: J Chris
authors: JC
authors: Pires
authors: Andre
authors: A
authors: Chanderbali
authors: Douglas E
authors: DE
authors: Soltis
authors: Srikar
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authors: Chamala
authors: Brad
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authors: Tomkins
authors: Claude W
authors: CW
authors: dePamphilis
authors: Rod A
authors: RA
authors: Wing
authors: Jim
authors: J
authors: Leebens-Mack
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