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Chloroplast Gene Database
  The dePamphilis Lab, Department of Biology, Penn State University


The chloroplast is the green plastid in land plants, algae and some protists. As the site in the cell where photosynthesis takes place, chloroplasts are responsible for much of the world's primary productivity, making chloroplasts essential to the lives of plants and animals alike. Agriculture, animal farming, and fossil fuels such as coal and oil are all "products" of photosynthesis that took place in chloroplasts. Other important activities that occur in chloroplasts (and several non-photosynthetic plastid types) include the production of starch, certain amino acids and lipids, some of the colorful pigments in flowers, and some key aspects of sulfur and nitrogen metabolism.

All plastids studied to date contain their own DNA, which is actually a reduced "genome" derived from a cyanobacterial ancestor that was captured early in the evolution of the eukaryotic cell. Land plant chloroplast genomes typically contain around 110-120 unique genes. Some algae have retained a large chloroplast genome with more than 200 genes, while the plastid genomes from nonphotosynthetic organisms may retain only a few dozen genes.

Putative protein-coding genes are designated as ORF followed by the number of amino acids, whereas ycf are those conserved in at least some other organisms. The term ycf is designated for a hypothetical chloroplast open reading frame.

This database contains annotated chloroplast/plastid genomes from the NCBI Organelle Genomes section at NCBI.

You can search for genes by their annotated names, conduct flexible BLAST searches, download protein and nucleotide sequences extracted from a selected chloroplast genome, and browse the putative protein families (tribes) created using TribeMCL.

If you use the data from the Chloroplast Genome Database (ChloroplastDB) in a publication, please cite our paper that describes the database:

L. Cui, N. Veeraraghavan, A.Richter, K. Wall, R. K. Jansen, J. Leebens-Mack, I. Makalowska, and C. W. dePamphilis. ChloroplastDB: the chloroplast genome database. Nucleic Acids Research, 2006, vol. 34, pp. D692-696.

We'd also appreciate hearing from you if you find this database useful, or if you have suggestions for ways we can improve the database.

Disclaimer: This database may contain annotation errors, conflicts or missing genes due to the uneven quality of GenBank annotations. If you have found such problems please report them to us.

Image from the public domain SWBIC biotech clipart.

Last database update on 21 June 2007