Populus is one of favorable model plants because of its small genome. Structural genomics of Populus has reached a breakpoint as nucleotides of the entire genome have been determined. Reaching the post genome era, functional genomics of Populus is getting more important for well-comprehended plant science. Development of bioresorce serving functional genomics is making rapid progress. Huge efforts have achieved deposits of expressed sequence tags (ESTs) in various plant species consequently accelerating functional analysis of genes. ESTs from full-length cDNA clones are especially powerful for accurate molecular annotation. We promoted collection and annotation of the ESTs from Populus nigra var. italica full-length enriched cDNA clones (PnFL clones) as part of functional genomics of tree species.
The RIKEN Populus database (RPOP DB) contains information of 10 Populus species (Populus deltoides, Populus euphratica, Populus tremula, Populus tremula x Populus alba, Populus tremula x Populus tremuloides, Populus tremuloides, Populus trichocarpa, Populus trichocarpa x Populus deltoides, Populus trichocarpa x Populus nigra and Populus x canadensis) other than our P.nigra. Their mRNA sequneces in GenBank / DDBJ / EMBL were cleaned, BLASTXed against 7 protein datasets and mapped to the P.trichocarpa genome (JGI 1.1).
Nanjo, T. and et al (2004) Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves. Plant Cell Physiol, 45: 1738-48 [Pubmed]
The mapped nucleotide sequences to the Populus trichocarpa genomic sequence (JGI 1.1) are available on GBrowse.
This database has a search function by optional keywords (e.g. kinase MAP) and accession ID including RIKEN PnFL clone ID (e.g. PnFL1-001_B16 BP921945 ).
Records in this database were obtained from the following datasets.
These are available for BLAST search.