Genome histories clarify evolution of the expansin superfamily: new insights from the poplar genome and pine ESTs

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Abstract
Expansins comprise a superfamily of plant cell wall-loosening proteins that has been divided into four distinct families, EXPA, EXPB, EXLA and EXLB. In a recent analysis of Arabidopsis thaliana and Oryza sativa expansins, we proposed a further subdivision of the families into 17 clades, representing independent lineages in the last common ancestor of monocots and eudicots. This division was based on both traditional sequence-based phylogenetic trees and on position-based trees, in which genomic locations and dated segmental duplications were used to reconstruct gene phylogeny. In this article we review recent work concerning the patterns of expansin evolution in angiosperms and include additional insights gained from the genome of a second eudicot species, Populus trichocarpa, which includes at least 36 expansin genes. All of the previously proposed monocot-eudicot orthologous groups, but no additional ones, are represented in this species. The results also confirm that all of these clades are truly independent lineages. Furthermore, we have used position-based phylogeny to clarify the history of clades EXPA-II and EXPA-IV. Most of the growth of the expansin superfamily in the poplar lineage is likely due to a recent polyploidy event. Finally, some monocot-eudicot clades are shown to have diverged before the separation of the angiosperm and gymnosperm lineages.