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Open Access Database

RepPop: a database for repetitive elements in Populus trichocarpa

Fengfeng Zhou12 and Ying Xu12*

Author Affiliations

1 Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA

2 BioEnergy Science Center, Tennessee, USA

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BMC Genomics 2009, 10:14  doi:10.1186/1471-2164-10-14

Published: 9 January 2009

Abstract

Background

Populus trichocarpa is the first tree genome to be completed, and its whole genome is currently being assembled. No functional annotation about the repetitive elements in the Populus trichocarpa genome is currently available.

Results

We predicted 9,623 repetitive elements in the Populus trichocarpa genome, and assigned functions to 3,075 of them (31.95%). The 9,623 repetitive elements cover ~40% of the current (partially) assembled genome. Among the 9,623 repetitive elements, 668 have copies only in the contigs that have not been assigned to one of the 19 chromosome while the rest all have copies in the partially assembled chromosomes.

Conclusion

All the predicted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.