Collection Citation
| Collection Title | RepPop: A Database for Repetitive Elements in Populus Trichocarpa | ||
| Collection Creator/PI | Zhou, Fengfeng; Xu, Ying | ||
| Collection Sponsor | USDOE - Office of Science (SC) | ||
| Other Sponsors | National Science Foundation (NSF); National Institutes of Health (NIH); Georgia Cancer Coalition | ||
| Host Website | University of Georgia, Computational and Systems Biology Lab | ||
| Other Related Organizations | University of Georgia; Oak Ridge National Laboratory (ORNL) | ||
| Main Content Type | Specialized Mix | ||
| Subject Categories | 59 - BASIC BIOLOGICAL SCIENCES | ||
| Keywords | Populus trichocarpa; Genome Sequencing; Eukaryotic Genomics; DNA transposons; RNA retrotransposons; Cellulose; Biomass; Biofuels | ||
| Description | The populus was selected as the first tree with the genome to be sequenced, mainly due to its small genome size, the wide deployment worldwide (30+ species), and its short juvenile period. Its rich content of cellulose, which is one of the most important source for biofuel. A female clone of P. trichocarpa was chosen to be sequenced. The current assembly of Populus genome is release 1.0, whose small insert end-sequence coverage is 7.5X, and it was released in June 2004. It consists of 22,012 sequences (including the 19 chromosomes) and the total length is 485,510,911 bps. The data was downloaded from the offical site of the Populus trichocarpa genome sequencing project. The latest version of the genome can be found at the Poplar Genome Project at JGI Eukaryotic Genomics. Duplication regions introduce significant difficulties into the correct assemblying of sequence contigs. We identified all the repetitive elements in the populus genome. We further assign each of them as different classes of repetitive elements, including DNA transposons, RNA retrotransposons, Miniature Inverted-repeat Transposable Elements (MITE), Simple Sequence Repeats (SSR), and Segmental Duplications (SD), etc. We organized the annotations into this easily browsable, searchable, and blastable database, RepPop, for the whole community.[From website for RepPop at http://csbl.bmb.uga.edu/~ffzhou/RepPop/] | ||
| DDE Number | DDE00328 | ||
| Special Interface | Yes | ||
| Registration_Required | No |
