.
About Populus trichocarpa
Populus trichocarpa (poplar) is a deciduous broadleaf tree that is native to Western North America. It is an economically important source of timber. Its rapid growth and compact genome size (approx. 500 Mbase, n=18) has lead to its use as a model organism for tree species.
Genome Sequencing and Gene Prediction (release Poptr JGI2.0)
The genome assembly of black cottonwood was published in 2006 [1]. Sequencing by the US department of Energy Joint Genome Institute (JGI) followed a whole genome shotgun strategy reaching 7.5x coverage, with scaffolds, where possible, being assigned to the genetic map. Gene predictions, by JGI, Oak Ridge National Laboratory (ORNL) and University of Ghent, combined 'known' poplar genes, protein homology-based and ab initio gene predictions using the JGI annotation pipeline. This browser presents the JGI v2 assembly (January 2010) and JGI v2.0 gene predictions (March 2010).
Gramene/Ensembl Genomes Annotation
Additional annotations generated by the Gramene/Ensembl Genomes projects include:
- The standard set of Gramene analyses detailed here.
- Phylogenetic gene trees and whole-genome alignments with several plant and metazoan species, using Ensembl's Compara pipeline.
- Probes from the Poplar Genome Array Affymetrix GeneChip were aligned to the genome using the Ensembl Functional Genomics pipeline.
This release of the assembly (JGI v2) for Populus trichocarpa is constructed with Arachne version 20071016HA with an attempt to merge the outbred haplotypes and an extensive attempt to remove contaminating sequence. The latest genetic mapping information was integrated to construct the 19 chromosome size scaffold. The total length of assembled sequences is 403 Mb, this includes
- 19 chromosomes with a total length of 370 Mb
- 2499 scaffolds with a total length of 33 Mb
Links
References
- Tuskan GA, Difazio S, Jansson S, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006;313(5793):1596-1604. PubMed ID: 16973872
.