Open Access Highly Accessed Open Badges 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

For all author emails, please log on.

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

Published: 23 October 2010

Additional files

Additional file 1:

Plastid tufA pseudogene in Isoetes flaccida. The tufA-like nucleotide sequence identified in the Isoetes flaccida plastome was aligned with the plastid encoded tufA sequence of Chara vulgaris using ClustalW [85]. An asterisk (*) indicates identical nucleotides and a dash (-) indicates insertion/deletion event (indel). A total 41% nucleotide similarity and 38 indels were identified.

Format: PDF Size: 543KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Angiosperm phylogenetic results using nucleotide data. The identical angiosperm topology was recovered using nucleotide data regardless of taxon set or analytical method. Nodes with bootstrap proportions (BP) = 100 or posterior probabilities (PP) = 1.0 are not shown (most nodes). Support was generally strong within the angiosperms with a few exceptions (shown). Nymphaea alba was always sister to remaining angiosperms, not Amborella trichopoda. Support for this was variable (BS = 78-90% depending on taxon set) and this has been addressed better elsewhere (Leebens-Mack et al.[80]). Mapped non-homoplastic indels are shown in yellow circles) and homoplastic indels are not shown.

Format: PDF Size: 84KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Phylogenetic results using inferred amino acid data. A) Cladogram based on ML analysis using RAxML of 49 inferred amino acid sequences from all 43 plastomes sampled (-ln = 181034.78356; Table 1). RAxML and BI analyses including all taxa as well as those excluding both Selaginella spp. and gnetophytes (-ln = 149105.09124) also converged on this topology. Numbers above the branches are ML bootstrap proportions and numbers below are Bayesian posterior probabilities in this order: all taxa included/Selaginella spp. excluded/gnetophytes excluded/Selaginella spp. and gnetophytes excluded. Support within the angiosperms was generally low in RAxML analyses. Nymphaea alba was always sister to remaining angiosperms, not Amborella trichopoda (not shown). B) and C) Phylograms based on RAxML analysis excluding either Selaginella spp. (-ln = 163523.52584) or gnetophytes (-ln = 166579.56793), respectively. In all phylogenetic analyses of inferred amino acid sequences angiosperms, gymnosperms, lycophytes, monilophytes and bryophytes (in the broad sense) were each monophyletic. However, two different best topologies were discovered depending on taxon set and analytical method. In all BI analyses regardless of taxon set as well as RAxML analyses including all taxa and excluding both Selaginella spp. and gnetophytes, the lycophytes were sister to seed plants and monilophytes were sister to all other land plants (including bryophytes) (Additional file 3). This relationship is inconsistent with most published phylogenies including our nucleotide sequence analyses. Branching order within the monilophytes differed from the topology found using nucleotide data in that Angiopteris evecta, Equisetum arvense and Psilotum nudum formed a paraphyletic grade with respect to Adiantum capillus-veneris and Alsophila spinulosa; E. arvense was sister to the leptosporangiate ferns and Angiopteris evecta was sister to the clade containing all other monilophytes. The position of Angiopteris evecta is inconsistent with previously published phylogenies [e.g., Pryer et al.[46]]. A different topology was found in RAxML analyses that excluded either Selaginella spp. or the gnetophytes (but not both). In these analyses, monilophytes were found sister to seed plants and bryophytes were sister to all other land plants (Additional file 3, 3). Although Angiopteris evecta, Equisetum arvense and Psilotum nudum still formed a paraphyletic grade, the relative positions of A. evecta and P. nudum were switched. Placement of A. evecta, E. arvense and P. nudum had high posterior probabilities (1.0 throughout), but bootstrap support for these clades was low. All nodes within the monilophyte clade had less than 65% support in RAxML bootstrap analyses except for the sister relationship between Adiantum capillus-veneris and Alsophila spinulosa.

Format: PDF Size: 162KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Insertion/deletion (indel) matrix Insertion/deletion events (indels) scored across the 49 aligned protein-coding genes used in this study. Characters were scored as 1 for presence or 0 for absence of a sequence stretch. Character state labels (CHARSTATELABELS) indicate in which gene the indel was identified and the position within that gene using the nucleotide alignment in Additional file 5.

Format: PDF Size: 328KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Nucleotide alignment Alignment of 49 genes from 43 plastomes used for phylogenetic analysis described in the text. Data are interleaved by gene and exclusion blocks are provided at the end of the file.

Format: TXT Size: 1.6MB Download file

Open Data