A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and Genomic Differences between the Monocot Orders Asparagales and Poales[W]

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.

FLOWERING LOCUS T genes control onion bulb formation and flowering

“…We set out to investigate whether FT-like genes are involved in controlling onion flowering and/or the photoperiodic induction of bulb formation. As the genome of onion has not been sequenced and there is only limited transcriptome data 29,30 , to identify FT-like transcripts, we performed GS-FLX sequencing of RNA isolated from the doubled haploid onion line CUDH2150. A BLAST search of our transcriptome data 31 identified six FT-like genes.…”

Phylogeny, Genome Size, and Chromosome Evolution of Asparagales

“…Recent studies (Kuhl et al 2004;Havey et al 2006) have found that nuclear sequences of expressed genes of Asparagus are more similar to those of the eudicot Arabidopsis than to Oryza, indicating that the grass genomes may not necessarily model the evolution of other monocot genomes. Here we discuss four areas of the phylogenetics and genomics of Asparagales: (1) phylogenetic relationships and morphological evolution of Asparagales in light of a new phylogenetic analysis based on seven loci (rbcL, atpB, trnL intron, trnL-F intergenic spacer, ndhF, matK, atpl); (2) chromosome evolution and genome size in Asparagales with an emphasis on Darlington's hypotheses on bimodal karyotypes; (3) genomic tools needed to infer mechanisms that can cause chromosomal evolution or change genome size; and (4) criteria for developing model taxa in Asparagales.…”

“…We might postulate that Asparagales genomes evolve similarly to grass genomes. However, grass genomes may not be representative of other genomes of the monocots, and in fact, recent evidence indicates that in some ways Asparagales genomes are more like that of Arabidopsis (Kuhl et al 2004;see Havey 2006). Given this, deciphering genome evolution in Asparagales is critical in understanding monocot evolution because of: (1) the incredible diversity of Asparagales (e.g., orchids); (2) the economic importance of Asparagales (e.g., onion, garlic, asparagus, aloe, yucca, ornamentals); and, (3) the phylogenetic position of Asparagales within monocots, because they bridge the gap between the well-studied Poales and Acorus L., the sister of the rest of the monocots, which is also now becoming a model taxon (Soltis et al 2002).…”

Genetic mapping of a major gene affecting onion bulb fructan content

“…Chloroform:sec octanol (24:1) was used instead of phenol/chloroform/isoamyl alcohol and tissue homogenisation and DNA pellet washes were performed as described earlier (McCallum et al 2001b). EST-SSR and SSCP markers were developed and evaluated as described previously (Kuhl et al 2004;Martin et al 2005;McCallum et al 2001b). Primer sets not reported in these previous publications are shown in Table 1.…”