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

Andrea Zuccolo, John E. Bowers, James C. Estill, Zhiyong Xiong, Meizhong Luo, Aswathy Sebastian, José L. Goicoechea, Kristi Collura, Yeisoo Yu, Yuannian Jiao, Jill Duarte, Haibao Tang, Saravanaraj Ayyampalayam, Steve Rounsley, Dave Kudrna, Andrew H. Paterson, J. C. Pires, Andre Chanderbali, Douglas E. Soltis, Srikar ChamalaBrad 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

Research output: Contribution to journalArticlepeer-review

25 Scopus citations

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. © 2011 Zuccolo et al.; licensee BioMed Central Ltd.
Original languageEnglish (US)
JournalGenome biology
Volume12
Issue number5
DOIs
StatePublished - May 27 2011
Externally publishedYes

Bibliographical note

Generated from Scopus record by KAUST IRTS on 2019-11-20

Fingerprint

Dive into the research topics of 'A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure'. Together they form a unique fingerprint.

Cite this