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Nucleic Acids Research Advance Access originally published online on April 8, 2008
Nucleic Acids Research 2008 36(9):3043-3053; doi:10.1093/nar/gkn095
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Nucleic Acids Research, 2008, Vol. 36, No. 9 3043-3053
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Lateral transfer of introns in the cryptophyte plastid genome

Hameed Khan and John M. Archibald*

Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

*To whom correspondence should be addressed. Tel: +1 902 494 2536; Fax: +1 902 494 1355; Email: john.archibald{at}dal.ca; jmarchib{at}dal.ca

Correspondence may also be addressed to Hameed Khan. Tel: +1 902 494 2536; Fax: +1 902 494 1355; Email: khanh{at}dal.ca

Received October 17, 2007. Revised January 17, 2008. Accepted February 16, 2008.

Cryptophytes are unicellular eukaryotic algae that acquired photosynthesis secondarily through the uptake and retention of a red-algal endosymbiont. The plastid genome of the cryptophyte Rhodomonas salina CCMP1319 was recently sequenced and found to contain a genetic element similar to a group II intron. Here, we explore the distribution, structure and function of group II introns in the plastid genomes of distantly and closely related cryptophytes. The predicted secondary structures of six introns contained in three different genes were examined and found to be generally similar to group II introns but unusually large in size (including the largest known noncoding intron). Phylogenetic analysis suggests that the cryptophyte group II introns were acquired via lateral gene transfer (LGT) from a euglenid-like species. Unexpectedly, the six introns occupy five distinct genomic locations, suggesting multiple LGT events or recent transposition (or both). Combined with structural considerations, RT–PCR experiments suggest that the transferred introns are degenerate ‘twintrons’ (i.e. nested group II/group III introns) in which the internal intron has lost its splicing capability, resulting in an amalgamation with the outer intron.


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