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RepPop: a database for repetitive elements in Populus trichocarpa.

Fengfeng Zhou¹, Ying Xu

¹Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. ffzhou@csbl.bmb.uga.edu

|January 13, 2009

Summary

This summary is machine-generated.

Researchers identified 9,623 repetitive elements in the Populus trichocarpa genome, assigning functions to over 30%. A new database, RepPop, aids in the assembly and characterization of these elements.

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Area of Science:

Genomics
Bioinformatics
Plant Science

Background:

The Populus trichocarpa genome was the first tree genome to be fully sequenced and is undergoing assembly.
Currently, there is a lack of functional annotation for repetitive elements within the Populus trichocarpa genome.

Purpose of the Study:

To identify and functionally annotate repetitive elements in the Populus trichocarpa genome.
To develop a publicly accessible database for these repetitive elements.

Main Methods:

Repetitive elements were computationally predicted within the Populus trichocarpa genome.
Functional assignments were made to the predicted repetitive elements.
A web-browsable database (RepPop) was created to store and query the data.

Main Results:

A total of 9,623 repetitive elements were predicted, with functions assigned to 3,075 (31.95%).
These elements constitute approximately 40% of the partially assembled genome.
The majority of repetitive elements have copies located on assembled chromosomes.

Conclusions:

The RepPop database provides a user-friendly platform for exploring Populus trichocarpa repetitive elements.
A community-driven Wiki system is integrated for ongoing functional annotation and curation.
RepPop is expected to significantly aid in the assembly and functional characterization of the Populus trichocarpa genome.