BDGP Resources

Materials: P1 Clones

P1 clone sequencing was stopped when it was determined that BAC clones were better substrates for sequencing and Whole Genome Shotgun sequence became available. BAC clones are better genomic clones to use.

DNA samples for construction of the BAC library and WGS plasmid libraries were prepared from the y; cn bw sp strain at about the same time in the summer of 1998. The Release 4 genome sequence derives from these libraries. The P1 library was constructed in 1991, and the y; cn bw sp strain evolved over those years. The primary difference between the BAC and whole genome shotgun libraries and the P1 library is the location of retrotransposons.

The BAC based physical map is more complete and accurate than the P1 map and has been verified by comparison to the whole genome shotgun sequence assembly. As the genome sequence is finished, sequence assemblies are verified by comparison to BAC restriction fingerprints.

Many of the P1 clones do not yield intact DNA in standard preps, due to the host strain genotype. Preparation of BAC DNA is much more reliable. Protocols for preparations of BAC DNA are available on the FlyBase in GBrowse.

Under "Feature tracks" at the bottom of the screen you can check the box next to "Tiling BAC" to see the BAC genomic clones that cover that region, and click "SHOW" next to "Tiling BAC in situ Image". In some cases this information is missing, but next to DataSource at the top left you can select the previous release to find BAC genomic clones for that region. You can then use the "Download sequence" options at the bottom of the screen to fetch the coordinates and sequence of the BAC clone.

P1 clones are no longer available. We thank the 13 laboratories that volunteered to distribute P1 clones during the 90's for their generous service.