Phylogenetic Relationships in Lycopersicon

The raw data from my Ph.D. thesis is available here in text file form. The DNA of 156 individual plants from 54 different accessions of 8 wild and domestic species of tomato was extracted, cut with 5 different restriction enzymes, Southern blotted, and probed with 40 different probes of known chromosomal location (10 probes from an EcoRI library, 15 probes from a PstI library, and 15 from a cDNA library). The fragment sizes were measured, and analyzed to determine the evolutionary relationships between the various species of wild and cultivated tomato.

The data in each file is arranged in columns, as follows:

  • Column 1: Individual plant number
  • Column 2: Species
  • Column 3: Accession Number or variety
  • Column 4: Subspecies
  • Column 5: Geographic location where accession was collected
  • Column 5: Probe (GeneticMarker)
  • Column 6: Enzyme DNA was cut with
  • Column 7, 8, etc.: Size of RFLP fragments seen

    For example:
    "33-3 L.peruvianum LA2150 L.peru.v.humifusum CajamarcaPeru TG27 EcoRI 6300 2140"
    means that plant number 33-3 was Lycopersicon peruvianum, accession number LA2150, subspecies (or variety) "humifusum." It was collected in Cajamarca, Peru, and the DNA, when probed with genetic marker TG27 onto DNA cut with EcoRI, produced 2 fragments, of 6300 and 2140 bp, respectively.

    There are forty text files, one containing the data for each probing with a chromosomal marker. For instance, "TG12.TXT" contains the data from the probing of TG12 onto all 156 plants cut with each of the 5 restriction enzymes.

    No, I cannot re-format the data for you. Please don't even ask.

    The Genetic Markers used as probes are:

    EcoRI-derived probes:
  • TG12
  • TG16
  • TG18
  • TG30
  • TG40
  • TG45
  • TG49
  • TG69
  • TG77
  • TG78

    PstI-derived probes:

  • TG14
  • TG17
  • TG20
  • TG21
  • TG24
  • TG26
  • TG27
  • TG31
  • TG41
  • TG42
  • TG46
  • TG54
  • TG61
  • TG62
  • TG63

    Single-copy cDNA probes:

  • CD05
  • CD10
  • CD17
  • CD19
  • CD39
  • CD53
  • CD57
  • CD58
  • CD59
  • CD60
  • CD64
  • CD67
  • CD70
  • CD72
  • CD77

    For further information on materials, methods, and results, see:

  • Miller, J.C., and S.D. Tanksley (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theoretical and Applied Genetics 80:437-448.
  • Miller, J.C., and S.D. Tanksley (1990) Effects of restriction enzymes, probe source, and probe length on detecting restriction fragment length polymorphism in tomato. Theoretical and Applied Genetics 80:385-389.

    RESTSITE:

  • Miller, Joyce C. (1991) RESTSITE: A phylogenetic program that sorts raw restriction data. Journal of Heredity 82:262-263.
  • Miller, Joyce C. (1990) Letter to the Editor Concerning a BASIC Program from J. Heredity 80:254. Journal of Heredity 81:493.
  • Nei, M., and J.C. Miller. (1990) A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics 125:873-879.

    For more information, you can e-mail me at:

    jmiller@genome.wi.mit.edu

    Last updated 5 June, 1996.

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