title: A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales.
abstract: 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.
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA.
authors.forename: Joseph C
authors.initials: JC
authors.lastname: Kuhl
authors.forename: Foo
authors.initials: F
authors.lastname: Cheung
authors.forename: Qiaoping
authors.initials: Q
authors.lastname: Yuan
authors.forename: William
authors.initials: W
authors.lastname: Martin
authors.forename: Yayeh
authors.initials: Y
authors.lastname: Zewdie
authors.forename: John
authors.initials: J
authors.lastname: McCallum
authors.forename: Andrew
authors.initials: A
authors.lastname: Catanach
authors.forename: Paul
authors.initials: P
authors.lastname: Rutherford
authors.forename: Kenneth C
authors.initials: KC
authors.lastname: Sink
authors.forename: Maria
authors.initials: M
authors.lastname: Jenderek
authors.forename: James P
authors.initials: JP
authors.lastname: Prince
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Havey
mesh_terms: 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
chemical_list: D004251:DNA Transposable Elements; D018076:DNA, Complementary; D003596:Cytosine; D019791:Guanidine