Aphid Genome Project

image: pea aphid
Shipher Wu (photograph) and Gee-way Lin (aphid provision), National Taiwan University [CC-BY-2.5 or CC-BY-2.5], via Wikimedia Commons

Publication and Data

International Aphid Genome Consortium

The BCM-HGSC would like to thank everyone in the International Aphid Genome Consortium, and others involved in the analysis and annotation of this genome that led to such an amazing set of publications. The genome and its analysis was published in the February issue of PLoS Biology "Genome Sequence of the Pea Aphid" Acyrthosiphon pisum by the International Aphid Genome Consortium.

Special Issue: Insect Molecular Biology
March 2010

Image of cover of Insect Molecular Biology, March 2010

Volume 19, Issue Supplement s2
Pages iii-iii, 1-272

Other Useful Links

Other useful links include AphidBase, which has blast resources, annotated genome browsers and other information, and phylomeDB where you can look at the phylogeny of aphid genes compared to other insects.

About the Project

The BCM-HGSC sequenced 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).

Genomic Resources

Data is released pre-publication under the rules of the Fort Lauderdale agreement. (see conditions for use statement, here and in the README). For the pea aphid genome in particular, the BCM-HGSC plans to publish an extensive analysis in collaboration with the pea aphid genome consortium. All interested researchers are welcome to join the consortium, to do so please go to http://www.as.miami.edu/iagc/ and take a look at the existing annotation groups, if you would like to join one of those groups, please email the group leader. If you would like to create a new annotation group on a subject not already covered by an existing group, please email the aphid genome consortium at aphidworkshop@bio.miami.edu. In this way we hope to prevent duplication of analyses within the aphid community, and allow by collaboration a fuller genome analyses than would otherwise be possible. Some (but not all) specific analyses that we believe fall fairly under the Ft Lauderdale agreements that are being performed by the pea aphid genome consortium include genome gene content comparison to other insects and sequenced organisms and genome comparison of primary and secondary symbionts and pea aphid host genomes, however a fuller list of the consortiums interests can be found at the signup site. Please feel free to join the consortium to add to this analysis.

Updates on the status, analysis and publication of the genome are being made available on the aphidgenomics listserv, if interested please join here. Information about conference phone calls discussing the project (phone numbers and times) is posted to the aphid genomics listserv. An annotation and analysis meeting is also planned for Princeton in July 2008—for details please go here.

Other useful websites include AphidBase. A gbrowse display of the aphid genome is at aphid base at INRA Rennes.

BCM-HGSC conditions of use

Genome Assembly

Release 2.0 of the Aphid Genome

Additional 454 data (SRA links):

SRX016526 was added to the pea aphid genome assembly, specifically to improve contig and scaffold N50s. The improved assembly is available from NCBI here.

Release 1.0 the Aphid Genome

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

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

Additional Resources

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

Pea aphid genome annotation workshops took place in 2008 and 2009. Details are at: http://www.as.miami.edu/iagc/.

Learn more about the pea aphid

Related Publications

Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol. 2010;8(2):e1000313. doi:10.1371/journal.pbio.1000313.

Shigenobu S, Richards S, Cree AG, et al. A full-length cDNA resource for the pea aphid, Acyrthosiphon pisum. Insect Mol Biol. 2010;19 Suppl 2:23-31. doi:10.1111/j.1365-2583.2009.00946.x.