Tempo and Mode in Evolution Genetics and Paleontology 50 Years After Simpson (1995) / Chapter Skim
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Genome Structure and Evolution in Drosophila: Applications of the Framework P1 Map
Genome Structure and Evolution in Drosophila: Applications of the Framework P1 Map
Pages 299-314
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From page 299... ...
A clone-based physical map also opens up new opportunities for studies of genome evolution. Clone-based physical maps have been assembled for several species chosen as model organisms in the Human Genome Project (Collins and Galas, 1993~.
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The in situ mapping strategy therefore requires that molecular overlaps be determined after the framework map is completed rather than during assembly. A physical map of the Drosophila genome based on yeast artificial chromosomes (YACs)
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cold to survive in medium containing 5% sucrose (Pierce et al., 1992~. Vector arms resulting from digestion of either vector with BamHI and Sca I were treated with calf intestinal alkaline phosphatase, and an equimolar ratio of vector-arm DNA and genomic DNA was ligated in the presence of T4 DNA ligase as described (Smoller et al., 1991~.
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PCR Amplification of Insert-Vector functions. STS markers were determined from sequences at the termini of the genomic fragments present in P1 clones after amplification by the polymerase chain reaction (PCR)
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First, a set of 96 reactions was carried out on DNA pools from all the clones present in each 8 x 12 array; each array containing a clone able to support amplification was subjected to a second set of 20 reactions carried out on DNA pools from clones in the 8 rows and 12 columns of the array. The DNA pools were prepared and generously provided by Bill Kimmerly and collaborators at Lawrence Berkeley Laboratories as part of the Drosophila Genome Center described in the acknowledgments.
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Because the average insert size of the clones is ~80 kb, the mapped clones with unique major sites of hybridization include ~200 megabase pairs (Mb) of DNA, or the equivalent of ~1.8 copies of the haploid euchromatic genome.
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Sections 1-20 comprise the X chromosome, 21~0 and 41-60 the respective left and right arms of chromosome 2, and 61-80 and 81-100 the respective left and right arms of chromosome 3. In each numbered section, the short vertical tick marks, from left to right, set off the lettered subdivisions A-F (unlabeled)
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From page 306... ...
The positions of the STS markers are indicated by vertical dashed lines intersecting with horizontal black bars below that represent P1 clones; the ability of a P1 clone to support amplification of a STS is indicated with a cross at the site of intersection. The P1 contigs are indicated by long horizontal black bars across the bottom.
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From page 307... ...
The principal limitation of cytological analysis is that, between species groups, the differences in banding patterns are usually too great for homologous chromosomal regions to be identified reliably, even between species whose morphological similarity implies virtual certainty of close relationship (Stone, 1962~. The result is a very incomplete understanding of the patterns, processes, and functional significance of genome evolution in Drosophila.
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308 W:° — t~ _ _ _ ; _ _ ~ ~ L _ ,_ 1 ~ · Olaf : _ ;;~ _ .— Z L .e _ _ it.
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309 ~r g it_ at: U,=\~==l C
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Numbered black bars across the top represent the polytene chromosome bands; narrow black bars below represent P1 clones. Positions of STS markers are denoted by dashed vertical lines intersecting P1 clones able to support PCR amplification.
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From page 311... ...
In addition to affording a common frame of reference for organizing diverse types of genetic data, physical maps also provide ready access to clones containing DNA sequences from any defined region of the genome. In this paper, we present a physical map of the genome of Drosophila melanogaster based on in situ hybridization with 2461 DNA fragments, averaging %80 kilobase pairs each, cloned in bacteriophage P1.
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The Drosophila Genome Center includes investigators at the University of California at Berkeley, Lawrence Berkeley Laboratories, Harvard University, and the Carnegie Institution of Washington in Baltimore. We are grateful to G
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(1992) The Drosophila genome project: Current status of the physical map.
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From page 314... ...
Nucleic Acids Res.
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