Aphid Genome Project
Shipher Wu (photograph) and
Gee-way Lin (aphid provision),
National Taiwan University
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
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 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
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 email@example.com. 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.
Conditions For Use - Statement also in the README file on the public FTP site
This data is made available before scientific publication with the following understanding:
The data may be freely downloaded, used in analyses, and repackaged in databases.
Users are free to use the data in scientific papers analyzing particular genes and small regions if the providers of this data are properly acknowledged. Please cite the BCM-HGSC web site or publications from BCM-HGSC referring to the genome sequence.
For analysis of multiple genes and larger regions, BCM HGSC plans to publish the assembly and genomic annotation of the dataset, including large-scale identification of regions of evolutionary conservation and request that groups either not publish such larger analyses, or join the aphid genome consortium to work with us in this endeavor.
This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects (see http://www.genome.gov/Pages/Research/WellcomeReport0303.pdf) and the resulting NHGRI policy statement.
Any redistribution of the data should carry this notice.
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.
Linearized chromosome and unplaced scaffold sequences
All unassembled reads including bin0 (reads with too few overlaps) and repeat reads
Traces are available from the NCBI Trace Archive, which can be searched using NCBI MegaBLAST with a same species or cross species query.
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 14th-15th, 2008. Details are at: http://www.as.miami.edu/iagc/.