D692–D696 Nucleic Acids Research, 2006, Vol. 34, Database issue doi:10.1093/nar/gkj055 ChloroplastDB: the Chloroplast Genome Database Liying Cui, Narayanan Veeraraghavan 1 , Alexander Richter1, Kerr Wall, Robert K. Jansen 2 , Jim Leebens-Mack, Izabela Makalowska1 and Claude W. dePamphilis* Department of Biology and Institute of Molecular Evolutionary Genetics, 1Center for Computational Genomics, Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA and 2Section of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA Received August 19, 2005; Revised and Accepted October 4, 2005 ABSTRACT The Chloroplast Genome Database (ChloroplastDB) is an interactive, web-based database for fully sequenced plastid genomes, containing genomic, protein, DNA and RNA sequences, gene locations, RNA-editing sites, putative protein families and align- ments (http://chloroplast.cbio.psu.edu/). With recent technical advances, the rate of generating new organ- elle genomes has increased dramatically. However, the established ontology for chloroplast genes and gene features has not been uniformly applied to all chloroplast genomes available in the sequence data- bases. For example, annotations for some published genome sequences have not evolved with gene nam- ing conventions. ChloroplastDB provides unified annotations, gene name search, BLAST and down- load functions for chloroplast encoded genes and genomic sequences. A user can retrieve all ortholog- ous sequences with one search regardless of gene names in GenBank. This feature alone greatly facilit- ates comparative research on sequence evolution including changes in gene content, codon usage, gene structure and post-transcriptional modifica- tions such as RNA editing. Orthologous protein sets are classified by TribeMCL and each set is assigned a standard gene name. Over the next few years, as the number of sequenced chloroplast gen- omes increases rapidly, the tools available in ChloroplastDB will allow researchers to easily identify and compile target data for comparative analysis of chloroplast genes and genomes. INTRODUCTION As the site in the eukaryotic 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. The oxygen in our atmo- sphere, all agricultural commodities and fossil fuels such as coal and oil are ‘products’ of photosynthesis (1). Other import- ant activities that occur in chloroplasts (and several types of non-photosynthetic plastids) include the production of starch (2), certain amino acids and lipids (3,4), some of the colourful pigments in ﬂowers (5), and key aspects of sulfur and nitrogen metabolism (6,7). All plastids studied to date contain their own distinct gen- omes derived from a cyanobacterial ancestor that was captured early in the evolution of the eukaryotic cell (8). Although much smaller than the nuclear genome, chloroplast genomes typically contain 110–120 unique genes including conserved open reading frames (ORFs) annotated as ycf genes (hypothet- ical chloroplast ORF) (9). Additional possible coding regions are designated as ORFs. These are typically annotated with the number of amino acids encoded (e.g., ORF1995) (10). Some algae have retained a large chloroplast genome with >200 genes, whereas the plastid genomes from non- photosynthetic organisms may retain only a few dozen genes. Chloroplast gene sequences have been widely used as gen- etic markers for plant and algal phylogenetic studies for nearly two decades (11,12). Whereas one or a few genes have been the focus of study most of this time [rbcL, atpB, matK; but see studies by Graham and Olmstead (13,14)], rapid growth in the number of chloroplast genome sequences is now making it possible for a wide range of phylogenetic issues to be addressed with genome scale datasets (15,16). For population-level studies, polymorphic regions for targeted sequencing can be identiﬁed through comparison of complete genome sequences for exemplar taxa (17). Chloroplast gen- ome sequences are also being used to address a wide range of evolutionary questions about changes in gene content and gene order (18), the dynamics of insertion and deletion events (19), intergenomic gene transfer (20) and photosynthetic evolution (21). The development of genetic transformation of chloro- plasts has been very exciting (22) and the list of target species will increase as the locations and ﬂanking sequences for inter- genic spacer regions are identiﬁed from an expanding number of chloroplast genome sequences (23). Genome-scale *To whom correspondence should be addressed. Tel: +1 814 863 6412; Fax: +1 814 865 9131; Email: cwd3@psu.edu The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. 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