title: Euchromatic and heterochromatic compositional properties emerging from the analysis of Solanum lycopersicum BAC sequences.
abstract: The consortium responsible for the sequencing of the tomato (Solanum lycopersicum) genome initially focused on the sequencing of the euchromatic regions using a BAC-by-BAC strategy. We analyzed the compositional features of the whole collection of BAC sequences publically available. This analysis highlights specific peculiarities of heterochromatic and euchromatic BACs, in particular: the whole BAC collection has i) a large variability in repeat and gene content, ii) a positive and significant correlation of LTR retrotransposons of the Gypsy class with the repeat content and iii) the preferential location of the SINEs (short interspersed nuclear elements) in BAC sequences showing a low repeat content. Our results point out a typical design of the tomato chromosomes and pave the way for further investigations on the relationship between DNA primary structure and chromatin organization in Solanaceae genomes.
authors.affiliation: University of Naples Federico II, Dept. of Soil, Plant, Environmental and Animal Production Sciences, Via Università 100, 80055 Portici, Italy. miriam.difilippo@gmail.com
authors.forename: Miriam
authors.initials: M
authors.lastname: Di Filippo
authors.forename: Alessandra
authors.initials: A
authors.lastname: Traini
authors.forename: Nunzio
authors.initials: N
authors.lastname: D'Agostino
authors.forename: Luigi
authors.initials: L
authors.lastname: Frusciante
authors.forename: Maria Luisa
authors.initials: ML
authors.lastname: Chiusano
mesh_terms: D001482:Base Composition / Q000502:physiology; D022202:Chromosomes, Artificial, Bacterial / Q000737:chemistry / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics*; D016000:Cluster Analysis; D018744:DNA, Plant / Q000235:genetics; D022041:Euchromatin / Q000235:genetics*; D006570:Heterochromatin / Q000235:genetics*; D018551:Solanum lycopersicum / Q000235:genetics*; D008969:Molecular Sequence Data; D018626:Retroelements / Q000235:genetics; D017422:Sequence Analysis, DNA; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics
chemical_list: D018744:DNA, Plant; D022041:Euchromatin; D006570:Heterochromatin; D018626:Retroelements