Conservation of gene repertoire but not gene order in pepper and tomato

Abstract

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...

Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers

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Comparative Genomics of Plant Chromosomes

“…Genetic analysis based on morphological and isoenzyme markers hinted at parallel arrangements of genes along the chromosomes of various taxa. These hints were later borne out at the DNA level, in seminal investigations of nightshades (Tanksley et al, 1988;Bonierbale et al, 1988) and grasses (Hulbert et al, 1990).…”

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“…Genetic analysis based on morphological and isoenzyme markers hinted at parallel arrangements of genes along the chromosomes of various taxa. These hints were later borne out at the DNA level, in seminal investigations of nightshades (Tanksley et al, 1988; Bonierbale et al, 1988) and grasses (Hulbert et al, 1990).Over the past two decades, multiple investigations of many additional taxa have delivered two broad messages: (1) In most plants, the evolution of the small but essential portion of the genome that actually encodes the organism's genes has proceeded relatively slowly; as a result, taxa that have been reproductively isolated for millions of years have retained recognizable intragenic DNA sequences as well as similar arrangements of genes along the chromosomes. (2) A wide range of factors, such as ancient chromosomal or segmental duplications, mobility of DNA sequences, gene deletion, and localized rearrangements, has been superimposed on the relatively slow tempo of chromosomal evolution and causes many deviations from colinearity.…”

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