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Retrotransposons and Tandem Repeat Sequences in the Nuclear Genomes of Cryptomonad Algae

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Abstract

The cryptomonads are an enigmatic group of unicellular eukaryotic algae that possess two nuclear genomes, having acquired photosynthesis by the uptake and retention of a eukaryotic algal endosymbiont. The endosymbiont nuclear genome, or nucleomorph, of the cryptomonad Guillardia theta has been completely sequenced: at only 551 kilobases (kb) and with a gene density of ∼1 gene/kb, it is a model of compaction. In contrast, very little is known about the structure and composition of the cryptomonad host nuclear genome. Here we present the results of two small-scale sequencing surveys of fosmid clone libraries from two distantly related cryptomonads, Rhodomonas salina CCMP1319 and Cryptomonas paramecium CCAP977/2A, corresponding to ∼150 and ∼235 kb of sequence, respectively. Very few of the random end sequences determined in this study show similarity to known genes in other eukaryotes, underscoring the considerable evolutionary distance between the cryptomonads and other eukaryotes whose nuclear genomes have been completely sequenced. Using a combination of fosmid clone end-sequencing, Southern hybridizations, and PCR, we demonstrate that Ty3-gypsy long-terminal repeat (LTR) retrotransposons and tandem repeat sequences are a prominent feature of the nuclear genomes of both organisms. The complete sequence of a 30.9-kb genomic fragment from R. salina was found to contain a full-length Ty3-gypsy element with near-identical LTRs and a chromodomain, a protein module suggested to mediate the site-specific integration of the retrotransposon. The discovery of chromodomain-containing retroelements in cryptomonads further expands the known distribution of the so-called chromoviruses across the tree of eukaryotes.

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Acknowledgments

We thank Iñaki Ruiz-Trillo and two anonymous reviewers for their helpful comments on the manuscript, Ignacio Marín for kindly providing a protein alignment of Ty3-gypsy reverse transcriptase domains, and Jessica Leigh for assistance with phylogenetic analysis. This work was supported by Genome Atlantic and an NSERC discovery grant (283335-2004) awarded to J.M.A. J.M.A. is a Scholar of the Canadian Institute for Advanced Research, Program in Evolutionary Biology.

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  1. Stan Theophilou

    Present address: DNA Technologies, 1721 Lower Water Street, Halifax, Nova Scotia, Canada, B3J 1S5

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  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, B3H 1X5

    Hameed Khan, Stan Theophilou & John M. Archibald

  2. The Atlantic Genome Centre, Institute for Marine Biosciences, Halifax, Nova Scotia, Canada

    Catherine Kozera, Bruce A. Curtis, Jillian Tarrant Bussey & Sharen Bowman

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Khan, H., Kozera, C., Curtis, B.A. et al. Retrotransposons and Tandem Repeat Sequences in the Nuclear Genomes of Cryptomonad Algae. J Mol Evol 64, 223–236 (2007). https://doi.org/10.1007/s00239-006-0088-9

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