Characterization of the tomato (Lycopersicon esculentum) genome using in vitro and in situ DNA reassociation

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Abstract
A detailed in vitro study of the kinetics of DNA renaturation, i.e., a C0t analysis, can be used to determine the size of a genome, the relative proportions of single-copy and repetitive sequences, and the complexity of genome components. Despite the dual importance of tomato (Lycopersicon esculentum) as a model for basic plant research and as a crop plant, to the best of our knowledge a C0t analysis has never been published for this species. This is probably due to difficulties associated with isolating sufficient quantities of polyphenol-free nuclear DNA from tomato. Recently we developed a technique for isolating milligram quantities of purified DNA from tomato nuclei, and we used DNA isolated in this manner to prepare a C0t curve for the tomato genome. Analysis of the C0t data indicates that the tomato genome (1C) consists of approximately 0.86 pg of DNA. In agreement with earlier molecular studies, the C0t analysis suggests that most (~73%) of the tomato genome is composed of single-copy sequences. Since 77% of the DNA in tomato chromosomes is found in constitutive heterochromatin, many of the single-copy sequences must reside in heterochromatin, an unexpected arrangement, considering that the constitutive heterochromatin of most species is predominantly repetitive DNA. To determine the distribution of repetitive and single-copy DNA along tomato pachytene chromosomes, we used hydroxyapatite-purified C0t fractions as probes for fluorescence in situ hybridization (FISH). Our FISH results indicate that highly repetitive DNA hybridizes almost exclusively with heterochromatin. While single-copy DNA comprises most of the DNA in euchromatin, heterochromatin contains the majority of single-copy DNA sequences, an observation consistent with our C0t data and previous cytological studies.Key words: tomato, Lycopersicon esculentum, genome size, heterochromatin, euchromatin, DNA reassociation, fluorescence in situ hybridization, FISH, C0t.