A BAC-based physical map of the Drosophila buzzatii genome

Abstract

Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps, and provide useful resources for sequencing entire genomes. Drosophila buzzatii is a representative species of the repleta group in the Drosophila subgenus, which is being widely used as a model in studies of genome evolution, ecological adaptation, and speciation. We constructed a Bacterial Artificial Chromosome (BAC) genomic library of D. buzzatii using the shuttle vector pTARBAC2.1. The library comprises 18,353 clones with an average insert size of 152 kb and an approximately 18x expected representation of the D. buzzatii euchromatic genome. We screened the entire library with six euchromatic gene probes and estimated the actual genome representation to be approximately 23x. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9555 clones, and assembled them using FingerPrint Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670 singletons. Finally, we anchored 181 large contigs (containing 7788 clones) to the D. buzzatii salivary gland polytene chromosomes by in situ hybridization of 427 representative clones. The BAC library and a database with all the information regarding the high coverage BAC-based physical map described in this paper are available to the research community.

Figure 1.

(A) Size distribution of the 9555 Drosophila buzzatii BAC clones analyzed by fingerprinting. (B) Distribution of clones in contigs and (C) contig sizes for the 345 contigs in the fingerprint map.

Figure 2.

Integrated BAC-based physical map of the Drosophila buzzatii genome. (We consider the cytological map to be a kind of physical map.) Vertical lines indicate the relative position of the 427 BAC clones that produced a primary hybridization signal and represent 181 contigs. Singletons are represented as discontinuous vertical lines. Clone names are shown above the chromosomes. Clone names separated by a bar were hybridized individually. Clone names with an asterisk indicate that two or three clones were hybridized as a mixture. The contigs to which the hybridized clones belong are represented by short horizontal segments below the chromosomes along with the contig number. The length of these segments is roughly proportional to contig size. See Supplemental Table S2 for details.