Phylotranscriptomic analysis of the origin and early diversification of land plants

Norman J. Wickett, Siavash Mirarab, Nam Nguyen, Tandy Warnow, Eric Carpenter, Naim Matasci, Saravanaraj Ayyampalayam, Michael S. Barker, J. Gordon Burleigh, Matthew A. Gitzendanner, Brad R. Ruhfel, Eric Wafula, Joshua P. Der, Sean W. Graham, Sarah Mathews, Michael Melkonian, Douglas E. Soltis, Pamela S. Soltis, Nicholas W. Miles, Carl J. RothfelsLisa Pokorny, A. Jonathan Shaw, Lisa De Gironimo, Dennis W. Stevenson, Barbara Surek, Juan Carlos Villarreal, Béatrice Roure, Hervé Philippe, Claude W. De Pamphilis, Tao Chen, Michael K. Deyholos, Regina S. Baucom, Toni M. Kutchan, Megan M. Augustin, Jun Wang, Yong Zhang, Zhijian Tian, Zhixiang Yan, Xiaolei Wu, Xiao Sun, Gane Ka Shu Wong, James Leebens-Mack

Research output: Contribution to journalArticle

Abstract

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances inmolecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the datamatrix or to phylogeneticmethod, including supermatrix, supertree, and coalescent-based approaches, maximumlikelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

Original languageEnglish (US)
Pages (from-to)E4859-E4868
JournalProceedings of the National Academy of Sciences of the United States of America
Volume111
Issue number45
DOIs
StatePublished - Nov 11 2014

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Embryophyta
Hepatophyta
Plant Genome
Bryophyta
Chlorophyta
Bayes Theorem
Phylogeny
Transcriptome
Blood Vessels
Seeds
Embryonic Structures
Genome
Amino Acids
Costs and Cost Analysis
DNA
Genes

Keywords

  • Land plants
  • Phylogenomics
  • Phylogeny
  • Streptophyta
  • Transcriptome

ASJC Scopus subject areas

  • General

Cite this

Phylotranscriptomic analysis of the origin and early diversification of land plants. / Wickett, Norman J.; Mirarab, Siavash; Nguyen, Nam; Warnow, Tandy; Carpenter, Eric; Matasci, Naim; Ayyampalayam, Saravanaraj; Barker, Michael S.; Burleigh, J. Gordon; Gitzendanner, Matthew A.; Ruhfel, Brad R.; Wafula, Eric; Der, Joshua P.; Graham, Sean W.; Mathews, Sarah; Melkonian, Michael; Soltis, Douglas E.; Soltis, Pamela S.; Miles, Nicholas W.; Rothfels, Carl J.; Pokorny, Lisa; Shaw, A. Jonathan; De Gironimo, Lisa; Stevenson, Dennis W.; Surek, Barbara; Villarreal, Juan Carlos; Roure, Béatrice; Philippe, Hervé; De Pamphilis, Claude W.; Chen, Tao; Deyholos, Michael K.; Baucom, Regina S.; Kutchan, Toni M.; Augustin, Megan M.; Wang, Jun; Zhang, Yong; Tian, Zhijian; Yan, Zhixiang; Wu, Xiaolei; Sun, Xiao; Wong, Gane Ka Shu; Leebens-Mack, James.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, No. 45, 11.11.2014, p. E4859-E4868.

Research output: Contribution to journalArticle

Wickett, NJ, Mirarab, S, Nguyen, N, Warnow, T, Carpenter, E, Matasci, N, Ayyampalayam, S, Barker, MS, Burleigh, JG, Gitzendanner, MA, Ruhfel, BR, Wafula, E, Der, JP, Graham, SW, Mathews, S, Melkonian, M, Soltis, DE, Soltis, PS, Miles, NW, Rothfels, CJ, Pokorny, L, Shaw, AJ, De Gironimo, L, Stevenson, DW, Surek, B, Villarreal, JC, Roure, B, Philippe, H, De Pamphilis, CW, Chen, T, Deyholos, MK, Baucom, RS, Kutchan, TM, Augustin, MM, Wang, J, Zhang, Y, Tian, Z, Yan, Z, Wu, X, Sun, X, Wong, GKS & Leebens-Mack, J 2014, 'Phylotranscriptomic analysis of the origin and early diversification of land plants', Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 45, pp. E4859-E4868. https://doi.org/10.1073/pnas.1323926111
Wickett, Norman J. ; Mirarab, Siavash ; Nguyen, Nam ; Warnow, Tandy ; Carpenter, Eric ; Matasci, Naim ; Ayyampalayam, Saravanaraj ; Barker, Michael S. ; Burleigh, J. Gordon ; Gitzendanner, Matthew A. ; Ruhfel, Brad R. ; Wafula, Eric ; Der, Joshua P. ; Graham, Sean W. ; Mathews, Sarah ; Melkonian, Michael ; Soltis, Douglas E. ; Soltis, Pamela S. ; Miles, Nicholas W. ; Rothfels, Carl J. ; Pokorny, Lisa ; Shaw, A. Jonathan ; De Gironimo, Lisa ; Stevenson, Dennis W. ; Surek, Barbara ; Villarreal, Juan Carlos ; Roure, Béatrice ; Philippe, Hervé ; De Pamphilis, Claude W. ; Chen, Tao ; Deyholos, Michael K. ; Baucom, Regina S. ; Kutchan, Toni M. ; Augustin, Megan M. ; Wang, Jun ; Zhang, Yong ; Tian, Zhijian ; Yan, Zhixiang ; Wu, Xiaolei ; Sun, Xiao ; Wong, Gane Ka Shu ; Leebens-Mack, James. / Phylotranscriptomic analysis of the origin and early diversification of land plants. In: Proceedings of the National Academy of Sciences of the United States of America. 2014 ; Vol. 111, No. 45. pp. E4859-E4868.
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AU - Carpenter, Eric

AU - Matasci, Naim

AU - Ayyampalayam, Saravanaraj

AU - Barker, Michael S.

AU - Burleigh, J. Gordon

AU - Gitzendanner, Matthew A.

AU - Ruhfel, Brad R.

AU - Wafula, Eric

AU - Der, Joshua P.

AU - Graham, Sean W.

AU - Mathews, Sarah

AU - Melkonian, Michael

AU - Soltis, Douglas E.

AU - Soltis, Pamela S.

AU - Miles, Nicholas W.

AU - Rothfels, Carl J.

AU - Pokorny, Lisa

AU - Shaw, A. Jonathan

AU - De Gironimo, Lisa

AU - Stevenson, Dennis W.

AU - Surek, Barbara

AU - Villarreal, Juan Carlos

AU - Roure, Béatrice

AU - Philippe, Hervé

AU - De Pamphilis, Claude W.

AU - Chen, Tao

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AU - Baucom, Regina S.

AU - Kutchan, Toni M.

AU - Augustin, Megan M.

AU - Wang, Jun

AU - Zhang, Yong

AU - Tian, Zhijian

AU - Yan, Zhixiang

AU - Wu, Xiaolei

AU - Sun, Xiao

AU - Wong, Gane Ka Shu

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