Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome

Eleven sequenced BACs were annotated and localized via FISH to tomato pachytene chromosomes - providing the first global insights into the compositional differences of euchromatin and pericentromeric heterochromatin in this model dicot species. The results indicate that tomato euchromatin has a gene density (6.7 kb/gene) similar to that of Arabidopsis and rice. Thus, while the euchromatin comprises only 25% of the tomato nuclear DNA, it is sufficient to account for approximate 90% of the estimated 38,000 non-transposon genes that comprise the tomato genome. Moreover, euchromatic BACs were largely devoid of transposons or other repetitive elements. In contrast, BACs assigned to the pericentromeric heterochromatin had a gene density 10-100 times lower than the euchromatin and are heavily populated by retrotransposons preferential to the heterochromatin - the most abundant transposons belonging to the Jinling Ty3/gypsy-like retrotransposon family. Jinling elements are highly methylated and rarely transcribed. Nonetheless, they have spread throughout the pericentromeric heterochromatin in tomato and wild tomato species fairly recently - well after tomato diverged from potato and other related solanaceous species. The implications of these findings on evolution and sequencing the genomes of tomato and other solanaceous species are discussed.

Key Words: Gene content, euchromatin, methylation, pericentromeric heterochromatin, retrotransposon

Online ISS 1091-6490
Copyright 2008 by the Genetics Society of America
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