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Unparalleled GC content in the plastid DNA of Selaginella

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Abstract

One of the more conspicuous features of plastid DNA (ptDNA) is its low guanine and cytosine (GC) content. As of February 2009, all completely-sequenced plastid genomes have a GC content below 43% except for the ptDNA of the lycophyte Selaginella uncinata, which is 55% GC. The forces driving the S. uncinata ptDNA towards G and C are undetermined, and it is unknown if other Selaginella species have GC-biased plastid genomes. This study presents the complete ptDNA sequence of Selaginella moellendorffii and compares it with the previously reported S. uncinata plastid genome. Partial ptDNA sequences from 103 different Selaginella species are also described as well as a significant proportion of the S. moellendorffii mitochondrial genome. Moreover, S. moellendorffii express sequence tags are data-mined to estimate levels of plastid and mitochondrial RNA editing. Overall, these data are used to show that: (1) there is a genus-wide GC bias in Selaginella ptDNA, which is most pronounced in South American articulate species; (2) within the Lycopsida class (and among plants in general), GC-biased ptDNA is restricted to the Selaginella genus; (3) the cause of this GC bias is arguably a combination of reduced AT-mutation pressure relative to other plastid genomes and a large number of C-to-U RNA editing sites; and (4) the mitochondrial DNA (mtDNA) of S. moellendorffii is also GC biased (even more so than the ptDNA) and is arguably the most GC-rich organelle genome observed to date—the high GC content of the mtDNA also appears to be influenced by RNA editing. Ultimately, these findings provide convincing support for the earlier proposed theory that the GC content of land-plant organelle DNA is positively correlated and directly connected to levels of organelle RNA editing.

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Acknowledgments

Many thanks to Robert W. Lee for insightful comments and to Jo Ann Banks for giving me permission to use the S. moellendorffii nuclear genome project trace file data. This work was supported by a grant to R.W.L. from the Natural Sciences and Engineering Research Council (NSERC) of Canada. D.R.S. is an Izaak Walton Killam Memorial Scholar and holds a Canada Graduate Scholarship from NSERC.

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  1. Department of Biology, Dalhousie University, Halifax, NS, Canada

    David Roy Smith

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  1. David Roy Smith
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Correspondence to David Roy Smith.

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Accession numbers

The GenBank accession numbers of the S. moellendorffii organelle genome sequences described in this study are FJ755183 (ptDNA) and GQ246802-GQ246808 (mtDNA).

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Smith, D.R. Unparalleled GC content in the plastid DNA of Selaginella . Plant Mol Biol 71, 627–639 (2009). https://doi.org/10.1007/s11103-009-9545-3

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