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First published online October 24, 2002; 10.1105/tpc.006155

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The Plant Cell, Vol. 14, 2659-2679, November 2002, Copyright © 2002,
American Society of Plant Biologists

GENOMICS ARTICLE

The Chlamydomonas reinhardtii Plastid Chromosome

Islands of Genes in a Sea of Repeats

Jude E. Maul1,a, Jason W. Lilly1,a, Liying Cuib, Claude W. dePamphilisb, Webb Millerb, Elizabeth H. Harrisc and David B. Stern2,a

a Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853
b Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
c Chlamydomonas Genetics Center, Department of Biology, Duke University, Durham, North Carolina 27708

2 To whom correspondence should be addressed. E-mail ds28{at}cornell.edu; fax 607-255-6695

Chlamydomonas reinhardtii is a unicellular eukaryotic alga possessing a single chloroplast that is widely used as a model system for the study of photosynthetic processes. This report analyzes the surprising structural and evolutionary features of the completely sequenced 203,395-bp plastid chromosome. The genome is divided by 21.2-kb inverted repeats into two single-copy regions of ~80 kb and contains only 99 genes, including a full complement of tRNAs and atypical genes encoding the RNA polymerase. A remarkable feature is that >20% of the genome is repetitive DNA: the majority of intergenic regions consist of numerous classes of short dispersed repeats (SDRs), which may have structural or evolutionary significance. Among other sequenced chlorophyte plastid genomes, only that of the green alga Chlorella vulgaris appears to share this feature. The program MultiPipMaker was used to compare the genic complement of Chlamydomonas with those of other chloroplast genomes and to scan the genomes for sequence similarities and repetitive DNAs. Among the results was evidence that the SDRs were not derived from extant coding sequences, although some SDRs may have arisen from other genomic fragments. Phylogenetic reconstruction of changes in plastid genome content revealed that an accelerated rate of gene loss also characterized the Chlamydomonas/Chlorella lineage, a phenomenon that might be independent of the proliferation of SDRs. Together, our results reveal a dynamic and unusual plastid genome whose existence in a model organism will allow its features to be tested functionally.




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