Open Access Highly Accessed Research article

Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

Kenneth G Karol1*, Kathiravetpillai Arumuganathan2, Jeffrey L Boore34, Aaron M Duffy5, Karin DE Everett6, John D Hall1, S Kellon Hansen5, Jennifer V Kuehl7, Dina F Mandoli68, Brent D Mishler9, Richard G Olmstead6, Karen S Renzaglia10 and Paul G Wolf5

Author Affiliations

1 The Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies, The New York Botanical Garden, Bronx, New York 10458, USA

2 Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA

3 Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

4 Genome Project Solutions, 1024 Promenade Street, Hercules, CA 94547, USA

5 Ecology Center and Department of Biology, Utah State University, Logan, UT 84322, USA

6 Department of Biology, University of Washington, Seattle, WA 98195, USA

7 Physical Biosciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA. 94720 USA

8 4500 NE 40th Street, Seattle, WA 98105, USA

9 Department of Integrative Biology and University and Jepson Herbaria, 1001 Valley Life Sciences Bldg., University of California, Berkeley, CA 94720, USA

10 Southern Illinois University, Plant Biology-SIUC, Mailcode: 6509, Carbondale, IL 62901, USA

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BMC Evolutionary Biology 2010, 10:321  doi:10.1186/1471-2148-10-321

Published: 23 October 2010



Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats.


We present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida, a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants), lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense), and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels). We found one new indel and an inversion of a block of genes that unites the monilophytes.


Monophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns," including Marattiaceae.