Abstract
BackgroundPopulus 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.ResultsWe 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.ConclusionAll 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.
Highlights
Populus trichocarpa is the first tree genome to be completed, and its whole genome is currently being assembled
Some repetitive elements have as high as 8,455 copies (RepPop694) in the Populus trichocarpa genome
We have provided a Wiki web site for the general user community to directly annotate and curate the assigned functions of repetitive elements and to keep track of updates of annotations of each repetitive element, using PmWiki [36]
Summary
Populus trichocarpa is the first tree genome to be completed, and its whole genome is currently being assembled. The Poplar was selected to be the first tree genome to be sequenced, mainly because of its extraordinarily rapid growth rate and its relatively compact genome size (450– 500 Mbps [1,2]). The Populus trichocarpa genome's rapid growth coupled with the high content of lignocelluloses has made it one of the model systems for the new generation of biofuels [4]. The current assembly of the Poplar genome was released in June 2004, and its total length is ~485 Mbps. The assembled 19 chromosomes with 7.66% gaps count for 63.41% of the whole genome. Further efforts are still needed to close the gaps in the sequenced chromosomes
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