Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/10/2003
Publication Date: 4/15/2004
Citation: Kuhl, J.C., Cheung, F., Yuan, Q., Martin, W.J., Zewdie, Y., Mccallum, J., Catanach, A., Rutherford, P., Sink, K., Jenderek, M.M., Prince, J.P., Town, C.D., Havey, M.J. 2004. Unique set of 11,008 onion (Allium cepa) ESTs reveals expressed sequence and genomic differences between monocot orders Asparagales and Poales. The Plant Cell. 16:114-125. Interpretive Summary: Enormous genetic resources have been developed for the grasses, including complete DNA sequence of rice. The Asparagales are the second most economically important monocot order and includes such economically important plants as asparagus, garlic, and onion. In spite of the relationship between the grasses and the Asparagales, it is not clear how useful genetic resources developed for the grasses will be useful for genetic improvement of the Asparagales. To assess DNA differences between the Asparagales and grasses, we sequenced 11,008 expressed genes from onion. Sequence analyses of these genes revealed many useful genetic markers for onion. Mean DNA similarity between rice and the Asparagales was 78% across coding regions. However comparisons of the expressed genes revealed strong differences between the Asparagales and grasses for important DNA characteristics. In fact, the Asparagales were more similar to eudicots than the grasses for these DNA characteristics. These results will be useful to plant geneticists interested in the evolution and genetic improvement of monocot crops.
Technical 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 genomic differences between the Asparagales and Poales, we generated 11,008 unique expressed sequence tags (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 the Poales for these genomic characteristics.