Summary
The major families of repeated DNA sequences in the genome of tomato (Lycopersicon esculentum) were isolated from a sheared DNA library. One thousand clones, representing one million base pairs, or 0.15% of the genome, were surveyed for repeated DNA sequences by hybridization to total nuclear DNA. Four major repeat classes were identified and characterized with respect to copy number, chromosomal localization by in situ hybridization, and evolution in the family Solanaceae. The most highly repeated sequence, with approximately 77000 copies, consists of a 162 bp tandemly repeated satellite DNA. This repeat is clustered at or near the telomeres of most chromosomes and also at the centromeres and interstitial sites of a few chromosomes. Another family of tandemly repeated sequences consists of the genes coding for the 45 S ribosomal RNA. The 9.1 kb repeating unit in L. esculentum was estimated to be present in approximately 2300 copies. The single locus, previously mapped using restriction fragment length polymorphisms, was shown by in situ hybridization as a very intense signal at the end of chromosome 2. The third family of repeated sequences was interspersed throughout nearly all chromosomes with an average of 133 kb between elements. The total copy number in the genome is approximately 4200. The fourth class consists of another interspersed repeat showing clustering at or near the centromeres in several chromosomes. This repeat had a copy number of approximately 2100. Sequences homologous to the 45 S ribosomal DNA showed cross-hybridization to DNA from all solanaceous species examined including potato, Datura, Petunia, tobacco and pepper. In contrast, with the exception of one class of interspersed repeats which is present in potato, all other repetitive sequences appear to be limited to the crossing-range of tomato. These results, along with those from a companion paper (Zamir and Tanksley 1988), indicate that tomato possesses few highly repetitive DNA sequences and those that do exist are evolving at a rate higher than most other genomic sequences.
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References
Arnheim N (1983) Concerted evolution of multigene families. In: Koehn R, Nei M (eds) Evolution of genes and proteins. Sinauer, Sunderland, pp 38–64
Bedbrook J, Jones J, O'Dell M, Thompson M, Flavell R (1980) A molecular description of telomeric heterochromatin in Secale species. Cell 19:545–560
Bennett MD, Smith JB (1976) Nuclear DNA amounts in Angiosperms. Philos Trans R Soc Lond [Biol] 274:227–274
Bernatzky R, Tanksley SD (1986a) Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898
Bernatzky R, Tanksley SD (1986b) Methods for detection of single or low copy sequences in tomato on Southern blots. Plant Mol Biol Rep 4:37–41
Bernatzky R, Tanksley SD (1986c) Majority of random cDNA clones correspond to single loci in the tomato genome. Mol Gen Genet 203:8–14
Birnboim HC (1983) A rapid alkaline extraction method for the isolation of plasmid DNA. Methods Enzymol 100:243–255
Cavalier-Smith T (1985) Eukaryote gene numbers, non-coding DNA and genome size. In: Cavalier-Smith T (ed) The evolution of genome size. Wiley, New York, pp 69–103
Chilton MD (1975) Ribosomal DNA in a nuclear satellite of tomato. Genetics 81:469–483
Clarke L, Carbon J (1976) A colony bank containing synthetic ColEl hybrid plasmids representative of the entire E. coli genome. Cell 9:91–99
Dover G (1982) Molecular drive: A cohesive mode of species evolution. Nature 284:111–117
Feinberg AP, Vogelstein B (1983) A technique for radiolabelling DNA restriction fragments to high specific activity. Anal Biochem 132:6–13
Flavell R (1980) The molecular characterization and organization of plant chromsomal DNA sequences. Annu Rev Plant Physiol 31:569–596
Flavell R (1986) Repetitive DNA and chromosome evolution in plants. Philos Trans R Soc Lond [Biol] 312:227–242
Galbraith DW, Harkins KR, Maddox JM, Ayres NM, Sharma DP, Firoozabady E (1983) Rapid flow cytometric analysis of the cell cycle in intact plant tissue. Science 220:1049–1051
Grunstein M, Hogness D (1975) Colony hybridization: A method for the isolation of cloned DNAs that contain a specific gene. Proc Natl Acad Sci USA 72:3961–3965
Gupta M, Bertram I, Shepherd NS, Saedler H (1983) Cinl, a family of dispersed repetitive elements in Zea mays. Mol Gen Genet 192:373–377
Gupta M, Shepherd NS, Bertram I, Saedler H (1984) Repetitive sequences and their organization on genomic clones of Zea mays. EMBO J 3:133–139
Hake S, Walbot V (1980) The genome of Zea mays, its organization and homology to related grasses. Chromosoma 79:251–270
Jones J, Flavell R (1982a) The mapping of highly repeated DNA families and their relationship to C-bands in chromosomes of Secale cereale. Chrosoma 86:595–612
Jones J, Flavell R (1982b) The structure, amount and chromosomal localization of defined repeated DNA sequences in species of the genus Secale. Chromosoma 86:613–641
Jorgensen RA, Cuellar RE, Thompson WF (1982) Modes and tempos in the evolution of ribosomal RNA genes in legumes. Carnegie Inst Yr Bk 81:98–101
Lapitan NLV, Sears RG, Rayburn Al, Gill BS (1986) Wheat-rye translocations: Detection of chromosome breakpoints by in situ hybridization with a biotin-labeled DNA probe. J Hered 77:415–419
Leutwiler LS, Hough-Evans BR, Meyerowitz EM (1984) The DNA of Arabidopsis thaliana. Mol Gen Genet 194:15–23
Litt M, White RL (1985) A highly polymorphic locus in human DNA revealed by cosmid-derived probes. Proc Natl Acad Sci USA 82:6206–6210
Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York
Martinez-Zapater J, Estelle M, Sommerville C (1986) A highly repeated DNA sequence in Arabidopsis thaliana. Mol Gen Genet 204:417–423
Pruitt RE, Meyerowitz EM (1986) Characterization of the genome of Arabidopsis thaliana. J Mol Biol 187:169–183
Rayburn AL, Gill BS (1985) Use of biotin-labeled probes to map specific DNA sequences on wheat chromosomes. J Hered 76:78–81
Rick CM (1971) Some cytogenetic features of the genome in diploid plant species. Stadler Genet Symp 1:153–174
Rivin C (1986) Analyzing genome variation in plants. Methods Enzymol 118:75–85
Scheller RM, Thomas RL, Lee AS, Klein WH, Niles WD, Britten RJ, Davidson EH (1977) Clones of individual sequences from sea urchin DNA constructed with synthetic EcoRI sites. Science 196:197–200
Schmid C, Jelinek W (1982) The AluI family of dispersed repetitive sequences. Science 216:1065–1070
Schweizer G, Ganal M, Ninnemann H, Hemleben V (1988) Species-specific DNA sequences for identification of somatic hybrids between Lycopersicon esculentum and Solanum acaule. Theor Appl Genet, in press
Smith G (1975) Evolution of repeated DNA sequences by unequal crossover. Science 191:528–535
Sugita M, Manzara T, Pichersky E, Cashmore A, Gruissem W (1987) Genomic organization, sequence analysis and expression of all five genes encoding the small subunit of ribulose-1,5-biphosphate carboxylase/oxygenase from tomato. Mol Gen Genet 209:247–256
Tanksley SD, Miller J, Paterson A, Bernatzky R (1987) Molecular mapping of plant chromsomes. Stadler Symp, in press
Tanksley SD, Bernatzky R, Lapitan NL, Prince JP (1988) Conservation of gene repertoire but not gene order in pepper and tomato. Proc Nat Acad Sci USA (in press)
Tautz D, Renz M (1983) An optimized freeze-squeeze method for the recovery of DNA fragments from agarose gels. Anal Biochem 132:14–19
Thompson WF, Murray MG (1981) The nuclear genome: structure and function. In: Strumpf PK, Conn EE (eds) Biochemistry of plants. Academic Press, New York, pp 10–81
Vallejos CE, Tanksley SD, Bernatzky R (1986) Localization in the tomato genome of DNA restriction fragments containing sequences homologous to the rDNA (45S), the major chlorophyll a/b binding polypeptide and the ribulose biphosphate carboxylase genes. Genetics 112:93–105
Zabel P, Meyer D, van de Stolpe O, van der Zaal B, Ramanna MS, Koornneef M, Krens F, Hille J (1985) Towards the construction of artificial chromosomes for tomato. In: van Vloten-Doting L, Groot GSP, Hall TC (eds) Molecular form and function of the plant genome. Plenum Press, New York, pp 609–624
Zamir D, Tanksley SD (1988) Tomato genome is comprised largely of fast evolving low copy number sequences. Mol Gen Genet 254–261
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Communicated by R.B. Goldberg
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Ganal, M.W., Lapitan, N.L.V. & Tanksley, S.D. A molecular and cytogenetic survey of major repeated DNA sequences in tomato (Lycopersicon esculentum). Mol Gen Genet 213, 262–268 (1988). https://doi.org/10.1007/BF00339590
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DOI: https://doi.org/10.1007/BF00339590