ARS | Publication request: Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 27, 2006
Publication Date: May 29, 2006
Citation: Wang, Y., Tang, X., Cheng, Z., Mueller, L., Giovannoni, J.J., Tanksley, S. 2006. Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome. Genetics. 172:2529-2540.

Interpretive Summary: Many plant and animal species possess chromosomes differentiated into highly condensed heterochromatin and largely decondensed euchromatic arms. In animals, heterochromatin is often associated with gene expression and suppressed genetic recombination, and contains a large number of repetitive sequences. In plants, more is known about the gene-rich euchromatin, but less about heterochromatin. Studies thus far suggest that plant heterochromatin, while gene-poor compared with euchromatin, still contains active genes, at least at certain times during the life cycle. This still leaves open several important questions: What are the functional differences between euchromatin and heterochromatin? Which of these differences are consistent among species and which are species-specific? What evolutionary forces have molded the composition and function of heterochromatin versus euchromatin? In hopes of shedding light on these questions, we have conducted a series of molecular cytogenetic experiments to characterize the nature of heterochromatin versus euchromatin in the model crop plant tomato. The answers to these questions will be important in determining the effectiveness of the international genome sequencing project which is focused on sequencing only the euchromatin of tomato as a model crop genome. In general, our results suggest that focusing sequencing efforts on the euchromatin should yield the majority of tomato genes as anticipated.

Technical Abstract: 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.