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.

Figure 1.

Distribution of GC Content for Large EST Data Sets of Arabidopsis, Onion, and Rice.

Figure 2.

GC Percentage Plots from 279 Homologous Full-Length Coding Regions of Arabidopsis versus Onion and Rice for the Entire Coding Region and for the First, Second, and Third Codon Positions. Onion data are shown with pink triangles, and rice data are shown with blue diamonds.

Figure 3.

Mean GC Content as a Function of Position (5′ to 3′) across 129-bp Sliding Windows for 279 Homologous Full-Length Sequences of Arabidopsis, Onion, and Rice.