GENOMICS APPROACHES FOR IMPROVING NUTRITIONAL QUALITY OF FOOD CROP SPECIES
Location: Plant, Soil and Nutrition Research
Title: Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato
| Datema, Erwin - PLANT RESEARCH INTRNL. |
| Mueller, Lukas - CORNELL |
| Buels, Robert - CORNELL |
| Visser, Richard - WAGENINGEN UNIV. |
| Stiekema, Willem - WAGENINGEN UNIV. |
| Vanham, Roeland - WAGENINGEN UNIV. |
Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 11, 2008
Publication Date: May 11, 2008
Citation: Datema, E., Mueller, L., Buels, R., Giovannoni, J.J., Visser, R., Stiekema, W., Vanham, R. 2008. Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. Biomed Central (BMC) Plant Biology. 8:34.
Interpretive Summary: Tomato (Solanum lycopersicon) and potato (S. tuberosum) are two economically important crop species, the genomes of which are currently being sequenced. This study presents a first genome-wide analysis of these two species, based on a large collection of BAC end sequences that represent approximately 19% and 10% of these genomes, respectively. The findings in this paper present a first glimpse into the evolution of Solanaceous genomes, both within the family, as relative to other plant species. Once the complete genome sequences of these species become available, whole-genome comparisons and protein- or repeat-family specific studies will be readily preformed.
The tomato genome has a higher repeat content than the potato genome, which is primarily the result of a higher amount of retrotransposons in the tomato genome. Potato has a higher abundance of simple sequence repeats than tomato, and the distribution of motifs also differs between these species. Furthermore, potato appears to contain approximately 6,400 more genes than tomato, and major gene families such as cytochrome P450 mono-oxygenases and serine-threonine protein kinases are significantly overrepresented in potato, compared to tomato. Moreover, the P450 superfamily appears to have expanded spectacularly in both species compared to Arabidopsis thaliana, suggesting an expanded network of secondary metabolic pathways in the Solanaceae. Both tomato and potato appear to have a low level of microsynteny with A. thaliana. A higher degree of synteny was observed with Populus trichocarpa, specifically in the region between 15.2 and 19.4 Mb on P. trichocarpa chromosome 10.