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Published online before print July 19, 2002, 10.1101/gr.341802
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Vol. 12, Issue 8, 1159-1167, August 2002

LETTER
Evidence That Plant-Like Genes in Chlamydia Species Reflect an Ancestral Relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast

Fiona S.L. Brinkman,1,2,3,12,13 Jeffrey L. Blanchard,4,5 Artem Cherkasov,3 Yossef Av-Gay,6 Robert C. Brunham,7 Rachel C. Fernandez,2 B. Brett Finlay,2 Sarah P. Otto,8 B.F. Francis Ouellette,9 Patrick J. Keeling,10 Ann M. Rose,3 Robert E.W. Hancock,2 and Steven J.M. Jones11

1 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6; 2 Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3; 3 Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada, V6H 3N1; 4 Promega Corporation, Madison, Wisconsin 53711, USA; 5 National Center for Genome Resources, Santa Fe, New Mexico 87505, USA; 6 Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada, V5Z 4E3; 7 University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada, V5Z 4R4; 8 Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4; 9 Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada, V5Z 4H4; 10 Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4; and 11 Genome Sequence Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 4E6

An unusually high proportion of proteins encoded in Chlamydia genomes are most similar to plant proteins, leading to proposals that a Chlamydia ancestor obtained genes from a plant or plant-like host organism by horizontal gene transfer. However, during an analysis of bacterial-eukaryotic protein similarities, we found that the vast majority of plant-like sequences in Chlamydia are most similar to plant proteins that are targeted to the chloroplast, an organelle derived from a cyanobacterium. We present further evidence suggesting that plant-like genes in Chlamydia, and other Chlamydiaceae, are likely a reflection of an unappreciated evolutionary relationship between the Chlamydiaceae and the cyanobacteria-chloroplast lineage. Further analyses of bacterial and eukaryotic genomes indicates the importance of evaluating organellar ancestry of eukaryotic proteins when identifying bacteria-eukaryote homologs or horizontal gene transfer and supports the proposal that Chlamydiaceae, which are obligate intracellular bacterial pathogens of animals, are not likely exchanging DNA with their hosts.

[Supplementary Material is available online at http://www.genome.org and at http://www.pathogenomics.bc.ca/BAE-watch.html.]

12 Corresponding author.

13 Present address: Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6.

12:1159-1167 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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