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Determing the complexity of a genome

We can calculate the complexity of a genome by measuring how long it takes for genomic DNA that has been denatured to reanneal. . C

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Determing the complexity of a genome

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    1. Determing the complexity of a genome Genomes have DNA sequences that occur with different frequencies. In other words, some DNA sequences only once and other DNA sequences are repeated many times in the same genome

    2. We can calculate the complexity of a genome by measuring how long it takes for genomic DNA that has been denatured to reanneal.

    5. The complexity of a sequence is defined as the longest non-repetitive sequence that can be derived from a sequence The complexity (X) of a population of uniformly-sized DNA molecules can be measured as follows: X= KC0t½ where X = the complexity of a uniform size population of DNA fragements

    7. If we rearrange the equation X= KC0t½ X/K= C0t½ we have an equation that relates C0t½ with the complexity of the genome

    8. Russel,P.J. (1986)Genetics Fig. 7-25a. Cot plots showing therenaturation of DNAs from organisms with small genomes: the bacterium E.coli, the bacterial viruses T2 and Lambda, and the animal virus SV40.

    9. Russel,P.J. (1986)Genetics Fig. 7-25b. Kinetics of renaturation of DNAfrom calf thymus and E. coli as seen in a Cot plot.

    10. highly repetitive, which reanneals very early in the reaction, and. middle repetitive, which anneals over more than 3 log C0t, single copy, which anneals at very high C0t values Note, single copy refers to 1- 10 copies per haploid genome Most genes are single copy DNA sequences; however, not all single copy sequences are genes

    11. Calculation of the complexity of a single class of DNA Let’s say we wanted to know how complex is the highly repetitive calf thymus DNA. Assuming that the highly repetitive DNA is 15% of the genome or 0.15. Let f =0.15, the fraction of highly repetitive DNA C0t½ (pure) = fC0t½ (mixture)

    12. Using substitution we get the following equation X = KC0t½ (pure) We can now determine the complexity of fraction of a genome.

    13. The total amount of DNA (size) in a haploid genome is called the C – value. The C – value does not correspond with the genome complexity This is known as the C- paradox See page 29 Fig. 1.14

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