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AGRICULTURAL SCIENCES
Estimating genome conservation between crop and model legume species

Hong-Kyu Choi  , Jeong-Hwan Mun  , Dong-Jin Kim  , Hongyan Zhu , Jong-Min Baek , Joanne Mudge ^¶, Bruce Roe ^||, Noel Ellis , Jeff Doyle , Gyorgy B. Kiss ^, , Nevin D. Young ^¶, and Douglas R. Cook ^, , ¶¶

Department of Plant Pathology and College of Agricultural and Environmental Sciences Genomics Facility, University of California, One Shields Avenue, Davis, CA 95616; ^¶Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108; ^||Advanced Center for Genome Technology, University of Oklahoma, Norman, OK 73019; John Innes Centre, Norwich NR4 7UH, United Kingdom; Department of Plant Biology, Cornell University, Ithaca, NY 14853; and Biological Research Center, Institute of Genetics, H-6701 Szeged, Hungary

Edited by Susan R. Wessler, University of Georgia, Athens, GA and approved August 13, 2004 (received for review March 30, 2004)

Legumes are simultaneously one of the largest families of crop plants and a cornerstone in the biological nitrogen cycle. We combined molecular and phylogenetic analyses to evaluate genome conservation both within and between the two major clades of crop legumes. Genetic mapping of orthologous genes identifies broad conservation of genome macrostructure, especially within the galegoid legumes, while also highlighting inferred chromosomal rearrangements that may underlie the variation in chromosome number between these species. As a complement to comparative genetic mapping, we compared sequenced regions of the model legume Medicago truncatula with those of the diploid Lotus japonicus and the polyploid Glycine max. High conservation was observed between the genomes of M. truncatula and L. japonicus, whereas lower levels of conservation were evident between M. truncatula and G. max. In all cases, conserved genome microstructure was punctuated by significant structural divergence, including frequent insertion/deletion of individual genes or groups of genes and lineage-specific expansion/contraction of gene families. These results suggest that comparative mapping may have considerable utility for basic and applied research in the legumes, although its predictive value is likely to be tempered by phylogenetic distance and genome duplication.

Abbreviations: BAC, bacterial artificial chromosome; NCBI, National Center for Biotechnology Information.

H.-K.C., J.-H.M., and D.-J.K. contributed equally to this work.

^¶¶ To whom correspondence should be addressed. E-mail: drcook{at}ucdavis.edu.

© 2004 by The National Academy of Sciences of the USA

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