Originally published as Genetics Published Articles Ahead of Print on June 18, 2006.

Genetics, Vol. 173, 2227-2235, August 2006, Copyright © 2006
doi:10.1534/genetics.105.049205

Analyses of Synteny Between Arabidopsis thaliana and Species in the Asteraceae Reveal a Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements

Lee Timms^*, Rosmery Jimenez^*, Mike Chase^*, Dean Lavelle, Leah McHale, Alexander Kozik, Zhao Lai, Adam Heesacker, Steven Knapp, Loren Rieseberg, Richard Michelmore and Rick Kesseli^*,1

^* Biology Department, University of Massachusetts, Boston, Massachusetts 02125, Genome Center and Department of Plant Sciences, University of California, Davis, California 95616, Biology Department, Indiana University, Bloomington, Indiana 47405 and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602

¹ Corresponding author: Biology Department, University of Massachusetts, 100 Morrissey Blvd., Boston, MA 02125.
E-mail: rick.kesseli{at}umb.edu

Comparative genomic studies among highly divergent species have been problematic because reduced gene similarities make orthologous gene pairs difficult to identify and because colinearity is expected to be low with greater time since divergence from the last common ancestor. Nevertheless, synteny between divergent taxa in several lineages has been detected over short chromosomal segments. We have examined the level of synteny between the model species Arabidopsis thaliana and species in the Compositae, one of the largest and most diverse plant families. While macrosyntenic patterns covering large segments of the chromosomes are not evident, significant levels of local synteny are detected at a fine scale covering segments of 1-Mb regions of A. thaliana and regions of <5 cM in lettuce and sunflower. These syntenic patches are often not colinear, however, and form a network of regions that have likely evolved by duplications followed by differential gene loss.

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