An Arabidopsis Polymorphism Database (NSF DEB 0723935)

Ümit Seren edited this page Mar 10, 2015 · 1 revision


The primary goal of this project, which is a collaboration between the groups of Nordborg, Gaut (UC Irvine), and Ware (CSHL), is to integrate the various sources of polymorphisms information currently being generated.

Project status

The A. thaliana and A. lyrata genomes plus all our SNP data are currently being imported into Gramene. The A. lyrata genome paper is just about to be published.

Original project abstract

The primary objective of this proposal is to generate a community resource for plant genetics by integrating several new data sets with the existing Arabidopsis thaliana genome sequence. In particular, the intention is to align the A. thaliana genome sequence with two other genome sequences that are currently being generated by DOE’s Joint Genome Institute, namely those of the two closely related species A. lyrata and Capsella rubella, and use the resulting alignment to illuminate the tremendous amounts of within-species variation data that are currently being generated for A. thaliana. The database containing all this information will make it possible to answer fundamental questions about the evolution of A. thaliana, and will facilitate the interpretation of the existing genome sequence, for example by revealing sequences that are evolutionarily conserved and therefore likely to be important. The project would greatly increase the value of data that already exist or are currently being generated. It is analogous to similar efforts to understand human variation and evolution by integrating vast amounts of human polymorphism data with genome sequences from closely related primates like chimpanzee and orangutan.

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