A BAC-based physical map of the major autosomes of Drosophila melanogaster

Science

Volumn 287, Issue 5461, 2000, Pages 2271-2274

  Hoskins, Roger A ^a   Nelson, Catherine R ^b   Berman, Benjamin P ^b   Laverty, Todd R ^b   George, Reed A ^a   Ciesiolka, Lisa ^a   Naeemuddin, Mohammed ^a   Arenson, Andrew D ^c   Durbin, James ^c   David, Robert G ^c   Tabor, Paul E ^c   Bailey, Michael R ^c   DeShazo, Denise R ^c   Catanese, Joseph ^d,e,f   Mammoser, Aaron ^d   Osoegawa, Kazutoyo ^d,e   De Jong, Pieter J ^d,e,f   Celniker, Susan E ^a   Gibbs, Richard A ^c   Rubin, Gerald M ^b   Scherer, Steven E ^c   more..

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

^d ROSWELL PARK CANCER INSTITUTE   (United States)

^e CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

^f PFIZER INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; CHROMOSOME; DROSOPHILA MELANOGASTER; GENE MAPPING; GENE SEQUENCE; IN SITU HYBRIDIZATION; NONHUMAN; POLYMERASE CHAIN REACTION; POLYTENE CHROMOSOME; PRIORITY JOURNAL; SEQUENCE TAGGED SITE;

ANIMALS; CENTROMERE; CHROMATIN; CHROMOSOMES, BACTERIAL; CLONING, MOLECULAR; CONTIG MAPPING; DNA FINGERPRINTING; DROSOPHILA MELANOGASTER; EUCHROMATIN; GENE LIBRARY; GENES, INSECT; GENETIC MARKERS; GENETIC VECTORS; GENOME; IN SITU HYBRIDIZATION; REPETITIVE SEQUENCES, NUCLEIC ACID; RESTRICTION MAPPING; SEQUENCE ANALYSIS, DNA; SEQUENCE TAGGED SITES; TELOMERE;

BACTERIA (MICROORGANISMS); DROSOPHILA MELANOGASTER; MELANOGASTER;

EID: 0034708791     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.287.5461.2271     Document Type: Article

References (36)

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16. A false negative rate of 5% was calculated as the fraction of probes designed from BAC end sequences that failed to hybridize to their source BAC. A false positive rate of 8% was estimated as follows: For each BAC with multiple locations in the map, we designated all STS hits except those at the most likely location to be false positives; the most likely map location was deemed the one with the most consecutive STS hits. We then divided the total number of false positive hits by the total number of hits in the complete data set to arrive at the false positive rate. We also calculated that 81% of BACs contained neither a single false negative nor a false positive.
17. Web fig. 1 (30) shows a sample region of the STS content map in the SEGMAP display format. The edited STS content maps were reformatted and displayed on the World Wide Web (5) by means of custom Java tools. This public version excludes BACs with an inferred false positive hit or more than one inferred false negative hit, unless such BACs are part of the sequenced tiling path.
18. 1 strain (6), partially digested with either Nde II or Hin DIII, and cloned in pBeloBAC11. Filters representing the 23,400 BACs in the library were hybridized and analyzed as described. Additional information on the Dros BAC library is available at www.hgmp.mrc.ac.uk/Biology/descriptions/ dros_bac.html.
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24. -6.
25. See information at www.hgsc.bcm.tmc.edu/drosophila/ mapping. As described by Marra et al. (25), the line drawings representing the fingerprint contigs may not accurately reflect the extent of BAC overlaps. Therefore, users should examine the IMAGE-processed gel lanes to verify BAC overlap; all files necessary for reassembly in FPC and fingerprint analysis are available. Web fig. 1 (30) shows STS content and restriction fingerprint assemblies in a sample region of the BAC map displayed in SEGMAP and FPC formats, respectively.
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30. E. W. Myers et al., Science 287, 2196 (2000). Comparison of the order of STS markers in this BAC map and the whole-genome shotgun sequence assembly identified 10 discrepancies in STS location (>99.5% concordance), not including differences in local STS order that are due to the limited resolution of STS content mapping. Three of these STS markers appear to hybridize to duplicated sequences, and the other seven cases may result from duplicated sequences or data-tracking errors. We have removed all 10 from the public version of the STS content map to avoid potential confusion. BAC order and overlap were not substantially affected by these edits.
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35. Instructions for preparing polytene chromosome in situ hybridizations are available at www.fruitfly.org/ methods/cytogenetics.html.
36. We thank A. Gnirke for advice on preparation of HMW DNA; J. McPherson for "overgo" oligonucleotide probe labeling and hybridization protocols; R. Zhang, T. Wells, and C. Hamerski for technical support; A. Loraine for her work on the ArmView and CytoView Web displays; S. Mullaney for photography and assistance with figures; and B. Kimmel for discussions at the planning stage. We acknowledge Imaging Research for software improvements resulting in the release of AIS v5.0. Finally, we thank all members of the Berkeley Drosophila Genome Project and Human Genome Sequencing Center for their support This work was supported by NIH grant HG00750 (to G.M.R.) and Howard Hughes Medical Institute (G.M.R. and T.R.L.).