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The Plant Cell, Vol. 14, 1441-1456, July 2002, Copyright © 2002,
American Society of Plant Biologists

GENOMICS ARTICLE

Deductions about the Number, Organization, and Evolution of Genes in the Tomato Genome Based on Analysis of a Large Expressed Sequence Tag Collection and Selective Genomic Sequencing

Rutger Van der Hoevena, Catherine Ronningb, James Giovannonic,d, Gregory Martind and Steven Tanksley1,a

a Department of Plant Breeding and Department of Plant Biology, Cornell University, Ithaca, New York 14850
b The Institute for Genomic Research, Rockville, MD 20850
c United States Department of Agriculture Plant, Soil, and Nutrition Laboratory, Cornell University, Ithaca, New York 14853
d Boyce Thompson Institute for Plant Research and Department of Plant Pathology, Cornell University, Ithaca, New York 14853

1 To whom correspondence should be addressed. E-mail sdt4{at}cornell.edu; fax 607-255-6683

Analysis of a collection of 120,892 single-pass ESTs, derived from 26 different tomato cDNA libraries and reduced to a set of 27,274 unique consensus sequences (unigenes), revealed that 70% of the unigenes have identifiable homologs in the Arabidopsis genome. Genes corresponding to metabolism have remained most conserved between these two genomes, whereas genes encoding transcription factors are among the fastest evolving. The majority of the 10 largest conserved multigene families share similar copy numbers in tomato and Arabidopsis, suggesting that the multiplicity of these families may have occurred before the divergence of these two species. An exception to this multigene conservation was observed for the E8-like protein family, which is associated with fruit ripening and has higher copy number in tomato than in Arabidopsis. Finally, six BAC clones from different parts of the tomato genome were isolated, genetically mapped, sequenced, and annotated. The combined analysis of the EST database and these six sequenced BACs leads to the prediction that the tomato genome encodes ~35,000 genes, which are sequestered largely in euchromatic regions corresponding to less than one-quarter of the total DNA in the tomato nucleus.




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