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MBE Advance Access published online on November 23, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj066
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted November 14, 2005

Research Article

Insight into the Diversity and Evolution of the Cryptomonad Nucleomorph Genome

Christopher E. Lane 1 * *, Hameed Khan 1 *, Melissa MacKinnon 1, Anna Fong 1, Stan Theophilou 2, and John M. Archibald 1

1 Genome Atlantic and the Canadian Institute for Advanced Research, Program in Evolutionary Biology. Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia CANADA
2 Genome Atlantic and the Canadian Institute for Advanced Research, Program in Evolutionary Biology. Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia CANADA; Present address: DNA Technologies, 1721 Lower Water Street, Halifax, Nova Scotia, Canada B3J 1S5

* To whom correspondence should be addressed.
Christopher E. Lane, E-mail: c.lane{at}dal.ca


  Abstract

The cryptomonads are an enigmatic group of marine and freshwater unicellular algae that acquired their plastids through the engulfment and retention of a eukaryotic ("secondary") endosymbiont. Together with the chlorarachniophyte algae, the cryptomonads are unusual in that they have retained the nucleus of their endosymbiont in a miniaturized form called a nucleomorph. The nucleomorph genome of the cryptomonad Guillardia theta has been completely sequenced and with only three chromosomes and a total size of 551 Kb, is a model of nuclear genome compaction. Using this genome as a reference, we have investigated the structure and content of nucleomorph genomes in a wide range of cryptomonad algae. In this study we have sequenced nine new cryptomonad nucleomorph 18S ribosomal DNA (rDNA) genes and four heat shock protein 90 (hsp90) gene fragments, and using pulsed-field gel electrophoresis and Southern hybridizations, have obtained nucleomorph genome size estimates for nine different species. We also used long-range PCR to obtain nucleomorph genomic fragments from Hanusia phi CCMP325 and Proteomonas sulcata CCMP704 that are syntenic with the subtelomeric region of nucleomorph chromosome I in G. theta. Our results indicate that (1) the presence of three chromosomes is a common feature of the nucleomorph genomes of these organisms, (2) nucleomorph genome size varies dramatically in the cryptomonads examined, (3) unidentified cryptomonad species CCMP1178 has the largest nucleomorph genome identified to date at ~845 Kb, (4) nucleomorph genome size reductions appear to have occurred multiple times independently during cryptomonad evolution, (5) the relative positions of the 18S rDNA, ubc4 and hsp90 genes are conserved in three different cryptomonad genera, and (6) interchromosomal recombination appears to be rapidly changing the size and sequence of a repetitive sub-telomeric region of the nucleomorph genome between the 18S rDNA and ubc4 loci. These results provide a glimpse into the genetic diversity of nucleomorph genomes in cryptomonads and set the stage for more comprehensive sequence-based studies in closely and distantly related taxa.

Keywords: nucleomorph; genome; cryptomonads; ribosomal RNA genes; evolution.

*These authors contributed equally to this work


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