Plant Cell Advance Online Publication
Published on December 11, 2003; 10.1105/tpc.017202
Received September 10, 2003
Accepted November 5, 2003
A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and
Genomic Differences between the Monocot Orders Asparagales and Poales
Joseph C. Kuhl 1, Foo Cheung 2, Qiaoping Yuan 2, William Martin 3, Yayeh Zewdie 4, John McCallum 5, Andrew Catanach 5, Paul Rutherford 6, Kenneth C. Sink 1, Maria Jenderek 7, James P. Prince 4, Christopher D. Town 2, and Michael J. Havey 3*
1
Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
2
The Institute for Genomic Research, Rockville, Maryland 20850
3
Agricultural Research Service, United States Department of Agriculture, Vegetable
Crops Unit, Department of Horticulture, University of Wisconsin, Madison, Wisconsin
53706
4
Department of Biology, California State University, Fresno, California 93740
5
Crop and Food Research, Private Bag 1074, Christchurch, New Zealand
6
Applied Management and Computing Division, Lincoln University, Lincoln, New Zealand
7
Agricultural Research Service, United States Department of Agriculture, National
Arid Land Plant Genetic Resources Unit, Parlier, California 93648
* To whom correspondence should be addressed. E-mail: mjhavey{at}wisc.edu.
Enormous genomic resources have been developed for plants in the monocot order Poales;
however, it is not clear how representative the Poales are for the monocots as a
whole. The Asparagales are a monophyletic order sister to the lineage carrying the
Poales and possess economically important plants such as asparagus, garlic, and onion.
To assess the genomic differences between the Asparagales and Poales, we generated
11,008 unique ESTs from a normalized cDNA library of onion. Sequence analyses of
these ESTs revealed microsatellite markers, single nucleotide polymorphisms, and
homologs of transposable elements. Mean nucleotide similarity between rice and the
Asparagales was 78% across coding regions. Expressed sequence and genomic comparisons
revealed strong differences between the Asparagales and Poales for codon usage and
mean GC content, GC distribution, and relative GC content at each codon position,
indicating that genomic characteristics are not uniform across the monocots. The
Asparagales were more similar to eudicots than to the Poales for these genomic characteristics.
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