Drosophila pseudoobscura Genome Project
Drosophila pseudoobscura Genome Project
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Drosophila pseudoobscura Photo, Dr. Stephen Schaeffer, Penn State University Featured Publications Links |
Updates
December 2012
We have upgraded the D. pseudoobscura assembly using Pacific Biosciences long read data.
With 24× mapped coverage of PacBio long-reads, we addressed 99% of gaps and were able to close 69% and improve 12% of all gaps in D. pseudoobscura.
For details, please see, "Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology"
December 2004
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 BCM-HGSC using the BCM-HGSC data link in the sidebar.
We would like to thank everyone involved in this great project.
About the Project
The BCM-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 BCM-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:
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:
BCM-HGSC BLAST
BCM-HGSC 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.
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]