The Chlamydomonas reinhardtii plastid chromosome

Islands of genes in a sea of repeats

Jude E. Maul, Jason W. Lilly, Liying Cui, Claude Walker Depamphilis, Webb Miller, Elizabeth H. Harris, David B. Stern

Research output: Contribution to journalArticle

287 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2659-2679
Number of pages21
JournalPlant Cell
Volume14
Issue number11
DOIs
StatePublished - Nov 1 2002

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Plastid Genomes
Chlamydomonas reinhardtii
Plastids
Islands
plastids
Chlamydomonas
Chromosomes
Genome
chromosomes
algae
genome
complement
Chlorella vulgaris
Chloroplast Genome
Genes
Chlorella
Chlorophyta
Intergenic DNA
genes
Nucleic Acid Repetitive Sequences

All Science Journal Classification (ASJC) codes

  • Plant Science
  • Cell Biology

Cite this

Maul, J. E., Lilly, J. W., Cui, L., Depamphilis, C. W., Miller, W., Harris, E. H., & Stern, D. B. (2002). The Chlamydomonas reinhardtii plastid chromosome: Islands of genes in a sea of repeats. Plant Cell, 14(11), 2659-2679. https://doi.org/10.1105/tpc.006155
Maul, Jude E. ; Lilly, Jason W. ; Cui, Liying ; Depamphilis, Claude Walker ; Miller, Webb ; Harris, Elizabeth H. ; Stern, David B. / The Chlamydomonas reinhardtii plastid chromosome : Islands of genes in a sea of repeats. In: Plant Cell. 2002 ; Vol. 14, No. 11. pp. 2659-2679.
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Maul, JE, Lilly, JW, Cui, L, Depamphilis, CW, Miller, W, Harris, EH & Stern, DB 2002, 'The Chlamydomonas reinhardtii plastid chromosome: Islands of genes in a sea of repeats', Plant Cell, vol. 14, no. 11, pp. 2659-2679. https://doi.org/10.1105/tpc.006155

The Chlamydomonas reinhardtii plastid chromosome : Islands of genes in a sea of repeats. / Maul, Jude E.; Lilly, Jason W.; Cui, Liying; Depamphilis, Claude Walker; Miller, Webb; Harris, Elizabeth H.; Stern, David B.

In: Plant Cell, Vol. 14, No. 11, 01.11.2002, p. 2659-2679.

Research output: Contribution to journalArticle

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