A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales.
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.
Kuhl
Joseph C
JC
Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA.
Cheung
Foo
F
Yuan
Qiaoping
Q
Martin
William
W
Zewdie
Yayeh
Y
McCallum
John
J
Catanach
Andrew
A
Rutherford
Paul
P
Sink
Kenneth C
KC
Jenderek
Maria
M
Prince
James P
JP
Town
Christopher D
CD
Havey
Michael J
MJ
D003596:Cytosine / Q000378:metabolism; D004251:DNA Transposable Elements / Q000235:genetics; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D020224:Expressed Sequence Tags; D018745:Genome, Plant; D019791:Guanidine / Q000378:metabolism; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D019697:Onions / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA
D004251:DNA Transposable Elements; D018076:DNA, Complementary; D003596:Cytosine; D019791:Guanidine