Award Abstract #0421634
Sequence and Annotation of the Euchromatin of Tomato.

NSF Org:	DBI Division of Biological Infrastructure
Initial Amendment Date:	August 16, 2004
Latest Amendment Date:	April 27, 2007
Award Number:	0421634
Award Instrument:	Cooperative Agreement
Program Manager:	Diane Jofuku Okamuro DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences
Start Date:	September 1, 2004
Expires:	February 29, 2008 (Estimated)
Awarded Amount to Date:	$4402795
Investigator(s):	Steven Tanksley sdt4@cornell.edu (Principal Investigator) Stephen Stack (Co-Principal Investigator) James Giovannoni (Co-Principal Investigator) Joyce Van Eck (Co-Principal Investigator) Lukas Mueller (Co-Principal Investigator)
Sponsor:	Cornell University - State 373 Pine Tree Road Ithica, NY 14850 607/255-5014
NSF Program(s):	PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT, 9251, 9109, 7462
Program Element Code(s):	1329

ABSTRACT

The genome of tomato (Solanum lycopersicon) contains approximately 950 million base pairs of DNA, more than 75% of which is densely packed and largely devoid of genes. The majority of genes are found in long contiguous stretches of gene-rich DNA located on the distal portions of each chromosome arm. In this project, we will lay the foundation for the sequencing of the gene-rich regions of all 12 tomato chromosomes by an international consortium as part of the Solanaceae Genomics Project or "SOL" (http://www.sgn.cornell.edu/solanaceae-project/).

The project will generate sequences from a sheared tomato DNA library to gain more insight into the structure of the tomato genome, and sequence 400,000 Bacterial Artificial Chromosome (BAC) ends to generate a sequence connector database. In addition, 20 carefully chosen BACs from the 5 US chromosomes will be fully sequenced. Fluorescence in-situ hybridization (FISH) analysis will be performed with about 50 selected BACs to further define the gene-rich regions in tomato.

The Solanaceae Genome Network (SGN, http://www.sgn.cornell.edu/), a relational database and website devoted to the genomics of solanaceous species, will be expanded to accommodate and incorporate all of the sequencing, annotation and mapping information generated from this project.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

Barry, C. and Giovannoni, J.. "Ripening inhibition in the tomato Green-ripe mutant results from ectopic expression of a novel protein which disrupts ethylene signal transduction," Proc. Natl. Acad. Sci. USA, v.103, 2006, p. 7923.

Chang, S.-B., and Stack, S.M.. "TGR4, a novel tomato centromere-specific retrotransposon in the Solanum section Lycopersicon.," Report of the Tomato Genetics Cooperative, v.56, 2006, p. 15.

Fei, Z., Tang, X., Alba, R. and Giovannoni, J.. "Tomato Expression Database (TED): A suite of data presentation and analysis tools.," Nucl Acids Res (Database issue), v.34, 2006, p. D766.

Giovannoni, J.. "Fruit ripening mutants yield insights into ripening control," Curr. Opin. Plant Biol., v.10, 2007, p. 283.

Mueller, L.A., Mills, A.A., Skwarecki, B., Buels, R.M., Menda, N., Tanksley, S.D.. "The SGN comparative map viewer," Bioinformatics, v.24, 2008, p. 422.

Mueller, L.A., Tanksley, S.D., Giovannoni, J.J., Van Eck, J., Stack, S., Choi, D., Kim, B.D., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Seymour, G., Bishop, G., Bryan, G., Sharma, R., Khurana, et al.. "The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL).," Comp Funct Genom, v.6, 2005, p. 153.

Wang Y, Tang X, Cheng Z, Mueller L, Giovannoni J, Tanksley S.. "Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome.," Genetics, v.172, 2006, p. 2529.

Wu, F., Mueller, L., Crouzillat, D., and Petiard, V.. "Bioinformatics and phylogenetics to identify large sets of single copy, orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the euasterid plant clade," Genetics, v.174, 2006, p. 1407.

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