Chlamydomonas Chloroplast Genome and Transcriptome Analysis

The Genome Map of Chlamydomonas, Showing the Major Classes of Genes, Superimposed on a False-Color Image of a Chloroplast/Mitochondria Transcriptome DNA Microarray and an Epifluorescence Microscopy Image of Cells Expressing Green Fluorescent Protein in the Chloroplast. In this issue, Maul et al. and Lilly et al. present bioinformatic and functional analyses of the completed Chlamydomonas plastid genome. (GFP microscopic image courtesy of Yutaka Komine.) The sequencing of the Chlamydomonas chloroplast genome and genome analysis presented by Maul et al. (2002)is the result of a collaborative effort between researchers at three institutions (Jude Maul, Jason Lilly, and David Stern at the Boyce Thompson Institute, Cornell University, Ithaca, NY; Liying Cui, Claude dePamphilis, and Webb Miller at Pennsylvania State University, University Park, PA; and Elizabeth Harris at Duke University, Durham, NC). In addition to a complete annotation of the genome, Maul et al. (2002)performed a comparative analysis of the Chlamydomonas chloroplast with 13 other fully sequenced plastid genomes and 2 cyanobacterial genomes. A surprising finding was that >20% of the Chlamydomonas chloroplast genome consists of repetitive DNA that includes numerous classes of short dispersed repeats. The only other sequenced chloroplast genome found to share this feature was that of another chlorophyte, Chlorella vulgaris. The Chlamydomonas/Chlo-rella lineage also was found to be characterized by an accelerated rate of gene loss compared with other chloroplast lineages. This analysis reveals a highly dynamic and unusual chloroplast genome and a wealth of new data that will benefit studies of functional, structural, and com-parative genomics. In the second article, Lilly, Maul, and Stern conducted global gene expression analysis of the Chlamydomonas chloroplast and mitochondrial transcriptomes under a variety of environmental conditions. The results showed strong organellar transcriptional changes in response to abiotic stresses such as phosphate and sulfur limitation, including changes in the expression of genes known to be involved in post-transcriptional processing and regulation (e.g., RNA processing and translation initiation). The results sug-gest that chloroplast transcript abundance is fully integrated into the cell's signaling network. Future work using the tools and approach described by Lilly et al. (2002)will provide valuable insights into the coordination of organellar and nuclear gene expression. More information on Chlamydomonas genomics, as well as access to databases discussed in these articles, can be found at The Chlamydomonas Genetics Center World Wide Web site at http://www.biology.duke.edu/chlamy/. An interactive site featuring the Chlamydomonas chloroplast genome and relevant resources can be found at http://bti.cornell.edu/bti2/chlamyweb/.