Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments

Abstract

A collection of 9,990 single-pass nuclear genomic sequences, corresponding to 5 Mb of tomato DNA, were obtained using methylation filtration (MF) strategy and reduced to 7,053 unique undermethylated genomic islands (UGIs) distributed as follows: (1) 59% non-coding sequences, (2) 28% coding sequences, (3) 12% transposons-96% of which are class I retroelements, and (4) 1% organellar sequences integrated into the nuclear genome over the past approximately 100 million years. A more detailed analysis of coding UGIs indicates that the unmethylated portion of tomato genes extends as far as 676 bp upstream and 766 bp downstream of coding regions with an average of 174 and 171 bp, respectively. Based on the analysis of the UGI copy distribution, the undermethylated portion of the tomato genome is determined to account for the majority of the unmethylated genes in the genome and is estimated to constitute 61+/-15 Mb of DNA (approximately 5% of the entire genome)--which is significantly less than the 220 Mb estimated for gene-rich euchromatic arms of the tomato genome. This result indicates that, while most genes reside in the euchromatin, a significant portion of euchromatin is methylated in the intergenic spacer regions. Implications of the results for sequencing the genome of tomato and other solanaceous species are discussed.

Tracing the Evolution of the Floral Homeotic B- and C-Function Genes through Genome Synteny

“…The G + C content for the five BAC/TACs was approximately 34%. This value is lower than the average reported for tomato (37%), which has one of the lowest G + C contents of any plant species (Messeguer et al 1991; Wang et al 2005). …”

“…However, our data suggest that the Antirrhinum genome has a much higher density of TEs (24% of predicted genes are TEs) than that of other dicot species, including tomato (12–96% TEs of which are retroelements; Wang et al 2005), Arabidopsis (mobile elements constitute only 4–8% of the genome; Casacuberta and Santiago 2003), and chickpea (8.6%; Rajesh et al 2008). Many of the TEs identified here are unlike TEs previously characterized in Antirrhinum .…”

Transcriptome Analysis of the Cf-12-Mediated Resistance Response to Cladosporium fulvum in Tomato

“…The downregulation of transcription factors was also identified. For example, the OFP family Solyc09g065350.1 (Wang et al, 2005), another uncharacterized transcription factor, was downregulated to ~5-fold in both infection stages. This result suggests that transcription factors play a critical role in response, especially in the early response, to C. fulvum infection.…”

Genome Mapping and Molecular Breeding of Tomato

“…In fact, as most tomato genes are located in the euchromatic regions of the genome, which constitue only about one fourth of the tomato genome [484], this ratio is much smaller for the genetically active fraction of the genome. Tomato was the first plant species in which a disease resistance gene, pto , conferring resistance to bacterial speck caused by Pseudomonas syringae pv.…”

“…The tomato nuclear genome comprises 12 chromosomes and approximately 950 Mbp of DNA, containing 59% non coding sequences, 28% coding sequences, 11% transposons, and 2% organellar sequences [484]. Approximately 77% of the chromosomal DNA is comprised of centromeric heterochromatic regions, which are devoid of genes [484, 489].…”