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Plant Physiol, March 2003, Vol. 131, pp. 1018-1026
Syntenic Relationships between Medicago truncatula
and Arabidopsis Reveal Extensive Divergence of Genome
Organization1,[w]
Hongyan
Zhu,2
Dong-Jin
Kim,2
Jong-Min
Baek,
Hong-Kyu
Choi,
Leland C.
Ellis,
Helge
Küester,
W. Richard
McCombie,
Hui-Mei
Peng, and
Douglas R.
Cook*
Department of Plant Pathology, University of California, Davis,
California 95616 (H.Z., D.-J.K., J.-M.B., H.-K.C., D.R.C.);
Department of Biochemistry and Biophysics (L.C.E.) and Department of
Plant Pathology, Texas A&M University, College Station, Texas 77843 (H.-M.P.); Department of Genetics, Universitaet Bielefeld, D-33501
Bielefeld, Germany (H.K.); and Lita Annenberg Hazen Genome Sequencing
Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring
Harbor, New York 11724 (W.R.M.)
Arabidopsis and Medicago truncatula represent
sister clades within the dicot subclass Rosidae. We used genetic
map-based and bacterial artificial chromosome sequence-based approaches
to estimate the level of synteny between the genomes of these model
plant species. Mapping of 82 tentative orthologous gene pairs reveals a
lack of extended macrosynteny between the two genomes, although marker
collinearity is frequently observed over small genetic intervals.
Divergence estimates based on non-synonymous nucleotide substitutions
suggest that a majority of the genes under analysis have experienced
duplication in Arabidopsis subsequent to divergence of the two genomes,
potentially confounding synteny analysis. Moreover, in cases of
localized synteny, genetically linked loci in M.
truncatula often share multiple points of synteny with
Arabidopsis; this latter observation is consistent with the large
number of segmental duplications that compose the Arabidopsis genome.
More detailed analysis, based on complete sequencing and annotation of
three M. truncatula bacterial artificial
chromosome contigs suggests that the two genomes are related by
networks of microsynteny that are often highly degenerate. In some
cases, the erosion of microsynteny could be ascribed to the selective
gene loss from duplicated loci, whereas in other cases, it is due to
the absence of close homologs of M. truncatula genes in Arabidopsis.
1
This work was supported by the National Science
Foundation Plant Genome Research Program (grant no. 9872664 to
D.R.C.).
2
These authors contributed equally to the paper.
[w]
The online version of this article contains Web-only
data. The supplemental material is available at
www.plantphysiol.org.
*
Corresponding author; e-mail drcook{at}ucdavis.edu; fax
530-754-6617.
© 2003 American Society of Plant Biologists
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