A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure |
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Authors: | Andrea Zuccolo John E Bowers James C Estill Zhiyong Xiong Meizhong Luo Aswathy Sebastian José Luis Goicoechea Kristi Collura Yeisoo Yu Yuannian Jiao Jill Duarte Haibao Tang Saravanaraj Ayyampalayam Steve Rounsley Dave Kudrna Andrew H Paterson J Chris Pires Andre Chanderbali Douglas E Soltis Srikar Chamala Brad Barbazuk Pamela S Soltis Victor A Albert Hong Ma Dina Mandoli Jody Banks John E Carlson Jeffrey Tomkins Claude W dePamphilis Rod A Wing Jim Leebens-Mack |
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Affiliation: | Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA. |
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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. |
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