Euchromatic and heterochromatic compositional properties emerging from the analysis of Solanum lycopersicum BAC sequences

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 hi...

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Bibliographic Details
Published in:Gene 2012-05, Vol.499 (1), p.176-181
Main Authors: Di Filippo, Miriam, Traini, Alessandra, D'Agostino, Nunzio, Frusciante, Luigi, Chiusano, Maria Luisa
Format: Article
Language:English
Subjects:
bacterial artificial chromosomes
Base Composition - physiology
Chromosomes, Artificial, Bacterial - chemistry
Chromosomes, Artificial, Bacterial - genetics
Chromosomes, Plant - genetics
Cluster Analysis
DNA
DNA, Plant - genetics
Euchromatin
Euchromatin - genetics
Gene content
genes
Heterochromatin
Heterochromatin - genetics
Lycopersicon esculentum - genetics
Molecular Sequence Data
Repeat content
Repetitive elements
Retroelements - genetics
retrotransposons
Sequence Analysis, DNA
Short Interspersed Nucleotide Elements - genetics
Solanum lycopersicum
Tomato genome
tomatoes
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Summary: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. ► LTR retrotransposons and SINEs significantly correlate with the repeat content. ► Compositional properties of euchromatic and heterochromatic regions emerge from BAC sequences.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2012.02.044