We report the isolation and characterization of seven nuclear genes encoding polyphenol oxidase (PPO) in tomato (Lycopersicon esculentum cv. VFNT Cherry). The seven genes (PPOs A, A', B, C, D, E and F) fall into three structural classes (I, II, and III) based on Eco RI and Hind III restriction fragment length polymorphisms (RFLP). RFLP mapping and PFGE analysis demonstrated that the genes reside on chromosome 8, and may be clustered within a 165 kb region. Phage insert mapping demonstrated PPO E and PPO F (both class III), and PPOs B, D and A (classes I, II and I respectively) are grouped within separate 12.4 kb clusters. The complete nucleotide sequence was determined for each gene. Comparison to cDNAs revealed that the PPOs lack introns. A transcript of about 2 kb is expected for each PPO. Each PPO possesses a region encoding a transit peptide characteristic of polypeptides targeted to the thylakoid lumen. Predicted precursor polypeptides range in mass from 66 to 71 kDa and predicted mature polypeptides range from 57 to 62 kDa. All the PPOs encode two putative copper-binding sites characteristic of bacterial, fungal and mammalian tyrosinases. Five of the seven PPOs possess divergent DNA sequences in their 5' promoter regions. These flanking sequence differences may regulate the differential expression of PPO genes.

Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not clear how representative the Poales are for the monocots as a whole. The Asparagales are a monophyletic order sister to the lineage carrying the Poales and possess economically important plants such as asparagus, garlic, and onion. To assess the genomic differences between the Asparagales and Poales, we generated 11,008 unique ESTs from a normalized cDNA library of onion. Sequence analyses of these ESTs revealed microsatellite markers, single nucleotide polymorphisms, and homologs of transposable elements. Mean nucleotide similarity between rice and the Asparagales was 78% across coding regions. Expressed sequence and genomic comparisons revealed strong differences between the Asparagales and Poales for codon usage and mean GC content, GC distribution, and relative GC content at each codon position, indicating that genomic characteristics are not uniform across the monocots. The Asparagales were more similar to eudicots than to the Poales for these genomic characteristics.

Homologies of tomato and pepper genes have been compared, and genetic linkage maps have been constructed based on a common set of cDNA clones and selected single-copy genomic clones. We report here that the gene repertoire of these two species is highly conserved, yet the linear order of the genes on the chromosomes has been greatly modified. Although the two species share the same number of centromeres, the chromosomal regions around those centromeres have undergone extensive rearrangements. Accompanying the extensive chromosome rearrangement has been a change in locus number for approximately 12% of the loci detected by random cDNA clones. Duplicated loci within each genome are normally found on different chromosomes and are not confined to one species, thus ruling out gene duplication as an explanation for the 4-fold higher DNA content of pepper. At least one of the duplications occurred since the divergence of tomato and pepper from their last common ancestor.The family Solanaceae contains many well-known plant species, including tomato, potato, eggplant, tobacco, pepper, andjimsonweed (Datura). The haploid DNA content of these species varies greatly: from 0.74 pg in tomato to 2.76 pg in pepper (1), yet they share the same basic chromosome number (x = 12). Since the basic chromosome number is generally conserved in this family, the question arises whether the number and order of genes are also conserved. In mammals there is good evidence for conservation of gene order even among species as divergent as cats and humans (2, 3).A linkage map of tomato (Lycopersicon esculentum) chromosomes has recently been constructed based largely on loci detected by hybridization to cDNA clones and selected single-copy genomic clones (4, 5). To gain a better understanding of the organization and evolution of plant chromosomes, we now report construction of a genetic linkage map of pepper (Capsicum spp.) based on hybridization to the same clones used to develop the tomato map. The use of these molecular probes provides a rapid method for identifying and mapping orthologous genes* in reproductively isolated species, a prerequisite to comparing gene number and order. MATERIALS AND METHODSThe majority of the clones used for mapping both tomato and pepper chromosomes were from a cDNA library derived from tomato leaf mRNA (4). The loci detected by hybridization to these tomato cDNA clones are designated CD], CD2, etc. Additional cDNA clones used for mapping were derived from pepper leaf mRNA, and the loci detected are designated with the symbol PC. Random single-copy tomato genomic clones (0.5-3.0 kilobases) found to hybridize to both tomato and pepper were also used as a source of probes, and these loci are designated TG. Clones of several known genes were also used in the comparative mapping study: small subunit ribulose bisphosphate carboxylase (Rbcs), chlorophyll a/b binding polypeptide (Cab), alcohol dehydrogenase (Adh), and the 45S ribosomal subunit (R45S). The Rbcs and Cab clones were selected from cDNA and phage lib...