Skip to main content
Journal cover image

Phylotranscriptomic analysis of the origin and early diversification of land plants.

Publication ,  Journal Article
Wickett, NJ; Mirarab, S; Nguyen, N; Warnow, T; Carpenter, E; Matasci, N; Ayyampalayam, S; Barker, MS; Burleigh, JG; Gitzendanner, MA; Wafula, E ...
Published in: Proceedings of the National Academy of Sciences of the United States of America
November 2014

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 in molecular 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 data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood 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.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

Proceedings of the National Academy of Sciences of the United States of America

DOI

EISSN

1091-6490

ISSN

0027-8424

Publication Date

November 2014

Volume

111

Issue

45

Start / End Page

E4859 / E4868

Related Subject Headings

  • Transcriptome
  • Streptophyta
  • Sequence Alignment
  • Quantitative Trait, Heritable
  • Phylogeny
  • Genome, Plant
  • Gene Expression Profiling
  • Evolution, Molecular
  • DNA, Plant
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., … 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, 111(45), E4859–E4868. https://doi.org/10.1073/pnas.1323926111
Wickett, Norman J., Siavash Mirarab, Nam Nguyen, Tandy Warnow, Eric Carpenter, Naim Matasci, Saravanaraj Ayyampalayam, et al. “Phylotranscriptomic analysis of the origin and early diversification of land plants.Proceedings of the National Academy of Sciences of the United States of America 111, no. 45 (November 2014): E4859–68. https://doi.org/10.1073/pnas.1323926111.
Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America. 2014 Nov;111(45):E4859–68.
Wickett, Norman J., et al. “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, Nov. 2014, pp. E4859–68. Epmc, doi:10.1073/pnas.1323926111.
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, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GK-S, Leebens-Mack J. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America. 2014 Nov;111(45):E4859–E4868.
Journal cover image

Published In

Proceedings of the National Academy of Sciences of the United States of America

DOI

EISSN

1091-6490

ISSN

0027-8424

Publication Date

November 2014

Volume

111

Issue

45

Start / End Page

E4859 / E4868

Related Subject Headings

  • Transcriptome
  • Streptophyta
  • Sequence Alignment
  • Quantitative Trait, Heritable
  • Phylogeny
  • Genome, Plant
  • Gene Expression Profiling
  • Evolution, Molecular
  • DNA, Plant