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 Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010478.

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.

[1]  J. Cary,et al.  Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase , 1992, Plant Molecular Biology.

[2]  S. Tanksley,et al.  Majority of random cDNA clones correspond to single loci in the tomato genome , 1986, Molecular and General Genetics MGG.

[3]  G. Khush,et al.  Cytogenetic analysis of the tomato genome by means of induced deficiencies , 1968, Chromosoma.

[4]  R. Van der Hoeven,et al.  Identification, Analysis, and Utilization of Conserved Ortholog Set Markers for Comparative Genomics in Higher Plants Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010479. , 2002, The Plant Cell Online.

[5]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[6]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[7]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[8]  D. Adam.  Now for the hard ones , 2000, Nature.

[9]  U. Lagercrantz,et al.  Rapid evolution of the family of CONSTANS LIKE genes in plants. , 2000, Molecular biology and evolution.

[10]  C. Elsik,et al.  Comparative Genomics of Plant Chromosomes , 2000, Plant Cell.

[11]  S. Tanksley,et al.  Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[12]  D. Stern.  PERSPECTIVE: EVOLUTIONARY DEVELOPMENTAL BIOLOGY AND THE PROBLEM OF VARIATION , 2000, Evolution; international journal of organic evolution.

[13]  T. C. Nesbitt,et al.  fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. , 2000, Science.

[14]  T. Wood,et al.  A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. , 2000, Genome research.

[15]  John Quackenbush,et al.  The TIGR Gene Indices: reconstruction and representation of expressed gene sequences , 2000, Nucleic Acids Res..

[16]  Wen-Hsiung Li,et al.  Rates of Nucleotide Substitution in Angiosperm Mitochondrial DNA Sequences and Dates of Divergence Between Brassica and Other Angiosperm Lineages , 1999, Journal of Molecular Evolution.

[17]  Jody Hey,et al.  The limits of selection during maize domestication , 1999, Nature.

[18]  Bret J. Pearson,et al.  Recruitment of a hedgehog regulatory circuit in butterfly eyespot evolution. , 1999, Science.

[19]  E. Pennisi.  A Bonanza for Plant Genomics , 1998, Science.

[20]  J. Doebley,et al.  Transcriptional Regulators and the Evolution of Plant Form , 1998, Plant Cell.

[21]  W. Pearson,et al.  Characterization of the tomato (Lycopersicon esculentum) genome using in vitro and in situ DNA reassociation , 1998 .

[22]  S. Homma,et al.  Subcellular location of polyphenol oxidase in apples. , 1997, Bioscience, biotechnology, and biochemistry.

[23]  A. Tiburcio,et al.  Polyamine metabolism and its regulation , 1997 .

[24]  M. Taylor,et al.  Recent advances in polyamine research , 1997 .

[25]  J. Mol,et al.  The No Apical Meristem Gene of Petunia Is Required for Pattern Formation in Embryos and Flowers and Is Expressed at Meristem and Primordia Boundaries , 1996, Cell.

[26]  R. Wu,et al.  Transgenic rice plants harboring an introduced potato proteinase inhibitor II gene are insect resistant , 1996, Nature Biotechnology.

[27]  D. Peterson,et al.  DNA content of heterochromatin and euchromatin in tomato (Lycopersicon esculentum) pachytene chromosomes. , 1996, Genome.

[28]  James F. Smith.  Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL , 1993 .

[29]  G. Martin,et al.  High density molecular linkage maps of the tomato and potato genomes. , 1992, Genetics.

[30]  G. An,et al.  Expression of proteinase inhibitors I and II in transgenic tobacco plants: effects on natural defense against Manduca sexta larvae. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[31]  N. Brisson,et al.  Cloning, expression, and sequence conservation of pathogenesis-related gene transcripts of potato. , 1989, Molecular plant-microbe interactions : MPMI.

[32]  R. Fischer,et al.  Interaction of a DNA binding factor with the 5′‐flanking region of an ethylene‐responsive fruit ripening gene from tomato. , 1988, The EMBO journal.

[33]  M. King,et al.  Evolution at two levels in humans and chimpanzees. , 1975, Science.

[34]  R. W. Robinson,et al.  Genetic Activity in a Heterochromatic Chromosome Segment of the Tomato , 1964, Science.