A BAC-based physical map of the Drosophila buzzatii genome

Journal Article · Fri Mar 18 04:00:00 EST 2005 · Genome Research

DOI:https://doi.org/10.1101/gr.3263105· OSTI ID:862175

Gonzalez, Josefa; Nefedov, Michael; Bosdet, Ian; Casals, Ferran; Calvete, Oriol; Delprat, Alejandra; Shin, Heesun; Chiu, Readman; Mathewson, Carrie; Wye, Natasja; Hoskins, Roger A; Schein, JacquelineE; de Jong, Pieter; Ruiz, Alfredo

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. Drosophilabuzzatii 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 a {approx}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 {approx}23X. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9,555 clones, and assembled them using Finger Printed Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670singletons. Finally, we anchored 181 large contigs (containing 7,788clones) 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.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE; National Institutes of Health Grant 100000118621; Direccion General de Ensenanza Superior e Investigacion Cientifica GrantBMC2002-01708
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 862175
• Report Number(s): LBNL--57923; BnR: 400412000
• Journal Information: Genome Research, Journal Name: Genome Research Journal Issue: 6 Vol. 15
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
BAC Drosophila physical map
CHROMOSOMES
CLONING
CONSTRUCTION
CONTIGS
DIGESTION
DROSOPHILA
ELECTROPHORESIS
FINGERS
GENES
IN-SITU HYBRIDIZATION
PROBES
SALIVARY GLANDS
VECTORS