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The evolution of chloroplast genes and genomes in ferns

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Abstract

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene order (a similar order that is ancestral in seed plants). We review the sequence of inversions that gave rise to this organization. We also explore global nucleotide substitution patterns in ferns versus those found in seed plants across plastid genes, and we review the high levels of RNA editing observed in fern plastomes.

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Acknowledgments

ALG and KMP are grateful to Lisa Bukovnik for advice on “second-generation” sequencing protocols and to Mohamed Noor for suggesting and facilitating the sequencing of Cheilanthes lindheimeri at Duke. Thanks to Mark Winston Ellis and Hardeep Rai for comments on the manuscript. This research was supported in part by NSF grant DEB-0717398 to KMP and DEB-0228432 to PGW.

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Authors and Affiliations

  1. Department of Biology, Utah State University, Logan, UT, USA

    Paul G. Wolf, Joshua P. Der, Aaron M. Duffy & Jacob B. Davidson

  2. Department of Biology, Duke University, Durham, NC, USA

    Amanda L. Grusz & Kathleen M. Pryer

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  1. Paul G. Wolf
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  2. Joshua P. Der
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  3. Aaron M. Duffy
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  4. Jacob B. Davidson
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  5. Amanda L. Grusz
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  6. Kathleen M. Pryer
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Correspondence to Paul G. Wolf.

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Supplementary Figure 1

Map depicting complete plastome of Cheilanthes lindheimeri. Genes on inside of circle are transcribed clockwise, those on the outside are transcribed counter-clockwise. Asterisks denote genes with introns. two asterisks denote a gene with two introns. Note that *rps12 is trans-spliced. (EPS 617 kb)

Supplementary Figure 2

Constraint tree used for analysis of substitution rates (EPS 381 kb)

Supplementary Table 1

Taxa used for nucleotide substitution rate analysis (DOC 244 kb)

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Wolf, P.G., Der, J.P., Duffy, A.M. et al. The evolution of chloroplast genes and genomes in ferns. Plant Mol Biol 76, 251–261 (2011). https://doi.org/10.1007/s11103-010-9706-4

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