Updates

December 2004 update:

A publication reporting this work, "Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene and cis-element evolution", has been published in Genome Research (January 2005). The annotated sequence is now available in Flybase (to query and to browse) and in GenBank. Supplemental information, including the filtered BlastZ alignments and the set of protein alignments used for dN/dS analysis, is also available from HGSC using the FTP Data link in the sidebar.

We would like to thank everyone involved in this great project.

Previous Updates

About the Project

HGSC has sequenced the second Drosophila species: Drosophila pseudoobscura, Genome Research. The euchromatic portion of the genome (125 Mb) was sequenced to approximately seven-fold coverage using a whole genome shotgun approach and is being assembled using the HGSC's assembly engine, Atlas. Comparison of this species assembly with the recently completed sequence of Drosophila melanogaster is expected to offer important further insights into the biology of this historic model for experimental genetics.

Project Goals:

• Library and Strain Info
• Generation of high quality paired-end sequencing reads from the following library sources:
• 2kb plasmid - 1.8 million reads completed
• 6kb plasmid - 770,000 reads
• 40kb fosmid - 45,000 reads
• 175kb BAC - 12,000 reads
• Generation of assembled draft and finished high-quality sequence for 16 fosmid projects
• Generation of 50,000 ESTs and 1,000 full-length cDNA sequences from Drosophila pseudoobscura cDNA libraries
• Generation of a whole genome assembly using the Atlas genome assembler
• Annotation of the Drosophila pseudoobscura genome, primarily by comparison to the finished Drosophila melanogaster genome

Access to the Data

• Assembly data is available using the sidebar links to:
• BLAST
• FTP Data
• Sequence Traces—NCBI Trace Archive link in the sidebar
• Annotated sequence—Flybase

International Genome Consortium Database

This project builds on the successful collaborative effort with the Berkeley Drosophila Genome Project (BDGP) and Celera Genomics to map and sequence the euchromatic portion of the Drosophila melanogaster genome—see the Drosophila melanogaster project page.

Conditions for use

Selected PubMed Citations

Richards, S, Liu, Y, Bettencourt, BR, Hradecky, P, Letovsky, S, Nielsen, R, Thornton, K, Hubisz, MJ, Chen, R et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.  Genome Res.  2005 Jan; 15(1):1-18. [PubMed]