Plant Molecular Biology

, Volume 76, Issue 3–5, pp 251–261 | Cite as

The evolution of chloroplast genes and genomes in ferns

  • Paul G. Wolf
  • Joshua P. Der
  • Aaron M. Duffy
  • Jacob B. Davidson
  • Amanda L. Grusz
  • Kathleen M. Pryer


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.


Inversion Phylogeny Plastid Plastome Substitution rates RNA editing 



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.

Supplementary material

11103_2010_9706_MOESM1_ESM.eps (618 kb)
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)
11103_2010_9706_MOESM2_ESM.eps (382 kb)
Supplementary Figure 2 Constraint tree used for analysis of substitution rates (EPS 381 kb)
11103_2010_9706_MOESM3_ESM.doc (244 kb)
Supplementary Table 1 Taxa used for nucleotide substitution rate analysis (DOC 244 kb)


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Paul G. Wolf
    • 1
  • Joshua P. Der
    • 1
  • Aaron M. Duffy
    • 1
  • Jacob B. Davidson
    • 1
  • Amanda L. Grusz
    • 2
  • Kathleen M. Pryer
    • 2
  1. 1.Department of BiologyUtah State UniversityLoganUSA
  2. 2.Department of BiologyDuke UniversityDurhamUSA

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