About the project

The HGSC is sequencing the pea aphid Acyrthosiphon pisum. The pea aphid displays both sexual and asexual reproduction, and is a model for bacterial endosymbiosis and developmental plasticity. It is also an important agricultural pest, quickly gaining resistance to multiple insecticides. The sequence will shed light on the evolution of resistance both to insecticides and host plant defenses and host plant defenses, suggest new tools for protecting crops. The sequencing strain was provided by David Stern's laboratory at Princeton University. The 525Mb genome is being sequenced using a whole genome shotgun strategy to a six-fold sequence coverage.

Sequencing of the pea aphid is funded by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH).

Access to the data

Genome Assembly

We have released a preliminary assembly. Acyr_1.0 is available for download. The assembly is described in detail in the README in that directory. This assembly is not optimal in terms of quality metrics (specifics of comparisons to an EST dataset and a small number of finished BACs are described in the README file) and is released as an interim dataset due to demand from the community.

Finished BAC sequences

A small number of BAC clones have been sequenced, finished and submitted to Genbank. These can be found here.

Blast Searches

HGSC

• Linearized chromosome and unplaced scaffold sequences
• Assembled contigs
• All unassembled reads including bin0 (reads with too few overlaps) and repeat reads

Traces are available from the NCBITrace Archive, which can be searched using NCBI MegaBLAST with a same species or cross species query.

Resources

White Paper

NCBI Taxonomy Browser

Conditions for use

Listserv

Updates about the aphid genome are being posted to the aphid genomics listserv. Please go to:
http://www.eco.princeton.edu/mailman/listinfo/aphidgenomics
to sign up.

Aphid Annotation Meeting

There will be an aphid genome annotation workshop in Princeton on
July 14-15, 2008. Details are at: http://www.as.miami.edu/AphidWorkshop