A useful tool for evolution studies: first physical genomic map of the Drosophila buzzatii

Brussels, 30 Jun 2005

An international team of researchers, led by the Universitat Autònoma de Barcelona (UAB), has published the first detailed physical map of the Drosophila buzzatii chromosomes. This fly species is a widely used model in studies of genome evolution.

The research was coordinated by Professor Alfredo Ruiz from the Department of Genetics and Microbiology of the UAB (Spain), and the team included investigators from the US and Canada.

In order to study and sequence the genome of large organisms, it is first necessary to break them into a large set of much smaller pieces, called clones, that overlap. These clones are obtained randomly from the genome, and must be organised into a physical map prior to any other manipulation. This is typically achieved using fingerprinting. Mapping will typically follow these steps:
- build a library of random extracts;
- build a fingerprint for each clone;
- compare fingerprints to detect overlaps;
- organise the clones into a map.

The investigation involved the construction of a Bacterial Artificial Chromosome (BAC) genomic library comprising more than 18,000 random fragments of the fly's genome injected within E. coli bacterial cells. Each bacterial clone carries one of these DNA fragments, about 150,000 nucleotides long, and can be multiplied in a laboratory culture to amplify the fly's DNA.

The second step involved arranging the random fragments present in the library in the same order and position as they are in the intact chromosomes. This means composing a puzzle with thousands of pieces. Two methods were used for this task. One of them is known as 'fingerprinting', and involves cutting the original clones into smaller fragments and then sizing these fragments by electrophoresis.

The fragments produced by different clones (their 'fingerprints') are compared with the help of computers, which allows the scientists to determine which clones overlap and therefore belong to the same chromosomal region. The second method, a technique known as 'in situ hybridization', required the hybridisation of the genomic clones to the giant salivary gland chromosomes of the larvae. The chromosomes of the Drosophila larval salivary glands are unusual in that their DNA undergo replication without division and become giant chromosomes consisting of a cable containing a high number of identical strands of DNA. This technique allows one to locate the position of each clone in the chromosome.

The interest value of this physical genomic map, one of the most detailed maps ever built in Drosophila, stems from the wide use of Drosophila buzzatii, a close relative of the fruit fly, in studies of genome evolution, ecological adaptation and speciation. The team has made available both the BAC library and a database with all information regarding the high coverage BAC-based physical map described in the paper to the international research community. From now on, thanks to the genomic library and the physical map, researchers will find it easier to compare the genomes of this and related species, and to assemble the reads when the genomes of these species are sequenced.

For further information, please contact:
Octavi López Coronado
Universitat Autònoma de Barcelona
E-mail: octavi.lopez@uab.es
Tel: +34 93 5813301
Remarks: Peer reviewed publication and references: A BAC-based physical map of the Drosophila buzzatii genome, Genome Research, June 2005.

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