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A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

Andrea Zuccolo1, John E Bowers2, James C Estill2, Zhiyong Xiong3, Meizhong Luo14, Aswathy Sebastian1, José Luis Goicoechea1, Kristi Collura1, Yeisoo Yu1, Yuannian Jiao5, Jill Duarte5, Haibao Tang267, Saravanaraj Ayyampalayam2, Steve Rounsley89, Dave Kudrna1, Andrew H Paterson27, J Chris Pires3, Andre Chanderbali10, Douglas E Soltis10, Srikar Chamala10, Brad Barbazuk10, Pamela S Soltis11, Victor A Albert12, Hong Ma135, Dina Mandoli14, Jody Banks15, John E Carlson16, Jeffrey Tomkins17, Claude W dePamphilis5, Rod A Wing1 and Jim Leebens-Mack2*

Author affiliations

1 Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA

2 Department of Plant Biology, University of Georgia, 4504 Miller Plant Sciences, Athens, GA 30602, USA

3 Department of Biological Sciences, University of Missouri, 371B Life Sciences Center, Columbia, MO 65211, USA

4 College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China

5 Intercollege Graduate Degree Program in Plant Biology and Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, 405 Life Sciences Building, University Park, Pennsylvania 16802, USA

6 Department of Plant and Microbiology, College of Natural Resources, University of California, 311 Koshland Hall, Berkeley 94709, CA, USA

7 Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30605, USA

8 School of Plant Sciences and BIO5, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA

9 Dow Agrosciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA

10 Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA

11 Florida Museum of Natural History, Museum Road and Newell Drive, University of Florida, Gainesville, FL 32611, USA

12 Department of Biological Sciences, University at Buffalo (SUNY), 637 Hochstetter Hall, Buffalo, NY 14260, USA

13 State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Plant Biology, Center for Evolutionary Biology, and Institutes of Biomedical Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China

14 Northern Lights, 4500 NE 40th Street, Seattle WA 98105, USA

15 Department of Botany and Plant Pathology, Purdue University, B028 Whistler Hall, West Lafayette, IN 47906, USA

16 School of Forest Resources, The Pennsylvania State University, 323 Forest Resources Building, University Park, PA 16802, USA

17 Clemson University Genomics Institute, Clemson University, 51 Cherry St, Clemson, NC 29634, USA

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Citation and License

Genome Biology 2011, 12:R48  doi:10.1186/gb-2011-12-5-r48

Published: 27 May 2011

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.