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Phylotranscriptomic analysis of the origin and early diversification of land plants
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Significance: Early branching events in the diversification of land plants and closely related algal lineages remain fundamental and unresolved questions in plant evolutionary biology. Accurate reconstructions of these relationships are critical for testing hypotheses of character evolution: for example, the origins of the embryo, vascular tissue, seeds, and flowers. We investigated relationships among streptophyte algae and land plants using the largest set of nuclear genes that has been applied to this problem to date. Hypothesized relationships were rigorously tested through a series of analyses to assess systematic errors in phylogenetic inference caused by sampling artifacts and model misspecification. Results support some generally accepted phylogenetic hypotheses, while rejecting others. This work provides a new framework for studies of land plant evolution.
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“In addition to our analyses, all the supermatrices have also been previously extensively analyzed using either RAxML or ExaML (e.g., Jarvis et al. 2014; Misof et al. 2014; Wickett et al. 2014).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Wickett et al. 2014
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ResultSelf-citationphylostratr : a framework for phylostratigraphy
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Phylogenomics and Plastome Evolution of the Chloridoid Grasses (Chloridoideae: Poaceae)
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“Taxon-removal analyses have been key in testing other phylogenies (Kelchner and Bamboo Phylogeny Group 2012; Parks et al. 2012; Wickett et al. 2014).”
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Protist Diversity and Eukaryote Phylogeny
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Self-citationAnalysis of the CYC / TB 1 class of TCP transcription factors in basal angiosperms and magnoliids
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“Although no sequences were found in members of the Charales, Chlorokybales, and Mesostigmatales, which occupy relatively basal branches in streptophyte phylogeny (Timme et al. 2012; Ruhfel et al. 2014; Wickett et al. 2014) and represented by a single sample in the 1,000 plants (1KP) data set, we cannot rule out the po…”
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“…Eaton and Ree, 2013; Smith et al., 2014), targeted enrichment of ultraconserved elements (UCEs) or conserved ortholog sequences (COS) (Mandel et al., 2014; Smith et al., 2014), and RNA-Seq (Wen et al., 2013; Wickett et al., 2014) could be suitable methods to resolve Hawaiian mint relationships.”
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InfluentialSelf-citationEvolution, Initiation, and Diversity in Early Plant Embryogenesis
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“…of protein-coding genes derived from RNAseq or full genomes have been used for inferring deep nodes in the tree of life, often analyzed at the amino acid level (Bapteste et al., 2002; Chiari et al., 2012; Wickett et al., 2014; Jarvis et al., 2014; Chen et al., 2015; Irisarri and Meyer, 2016).”
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Early Cretaceous Umkomasia from Mongolia: implications for homology of corystosperm cupules
Shi, G., Leslie, A. B., Herendeen, P. S., Herrera, F. A., Ichinnorov, N., Takahashi, M., Knopf, P., & Crane, P. R. (2016) · New Phytologist · doi:10.1111/nph.13871 · Cited by 51
Evolution of land plants: insights from molecular studies on basal lineages
Ishizaki, K. (2016) · Bioscience Biotechnology and Biochemistry · doi:10.1080/09168451.2016.1224641 · Cited by 51
“[4] Wickett NJ, Mirarab S, Nguyen N, et al.”
BackgroundWen, J., Harris, A., Ickert‐Bond, S. M., Dikow, R. B., Wurdack, K. J., & Zimmer, E. A. (2017) · Journal of Systematics and Evolution · doi:10.1111/jse.12270 · Cited by 50
Zhao, C., Lasses, T., Bako, L., Kong, D., Zhao, B., Chanda, B., Bombarely, A., Cruz‐Ramírez, A., Scheres, B., Brunner, A. M., et al. (2017) · New Phytologist · doi:10.1111/nph.14704 · Cited by 51
“A phylogeny of the XND1 group based on full -length proteins from diverse angiosperm s (Figs 1, S2) generally mirrored species phylogenies (Zeng et al., 2014; Wickett et al., 2014).”
BackgroundConserved redox‐dependent DNA binding of ROXY glutaredoxins with TGA transcription factors
Gutsche, N., Holtmannspötter, M., Maß, L., O'Donoghue, M., Busch, A. E., Lauri, A., Schubert, V., & Zachgo, S. (2017) · Plant Direct · doi:10.1002/pld3.30 · Cited by 50
“This basal land plant belongs together with mosses and hornworts to the bryophyte group, among which phylogenetic relationships are not yet unambiguously resolved (Qiu et al., 2006; Wickett et al., 2014).”
Plant phylogenomics based on genome-partitioning strategies: Progress and prospects
Yu, X., Yang, D., Guo, C., & Gao, L. (2018) · Acta Botanica Yunnanica · doi:10.1016/j.pld.2018.06.005 · Cited by 54
“through phylotranscriptomic (including 1KP data) analysis of 852 nuclear genes and 1,701,170 aligned sites (Wickett et al., 2014).”
MethodXue, L., Alabady, M., Mohebbi, M., & Tsai, C. (2015) · Tree Genetics & Genomes · doi:10.1007/s11295-015-0907-5 · Cited by 51
Evolutionary Genomics of Ferns and Lycophytes
Sessa, E. B., & Der, J. P. (2016) · Advances in botanical research · doi:10.1016/bs.abr.2016.02.001 · Cited by 50
Self-citationEvolution of floral diversity: genomics, genes and gamma
Chanderbali, A. S., Berger, B., Howarth, D. G., Soltis, P. S., & Soltis, P. S. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0509 · Cited by 53
Self-citationMikhailyuk, T. I., Lukešová, A., Glaser, K., Holzinger, A., Obwegeser, S., Nyporko, S., Friedl, T., & Karsten, U. (2018) · Protist · doi:10.1016/j.protis.2018.03.002 · Cited by 50
“Phylotranscriptomic analysis using up to 852 nuclear genes clearly demonstrated, that the Zygnematophyceae is the sister lineage to embryophytes with maximal support (Wickett et al. 2014).”
BackgroundMethodGardner, E. M., Johnson, M. G., Pereira, J. T., Puad, A. S. A., Arifiani, D., Sahromi, Wickett, N. J., & Zerega, N. J. C. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa073 · Cited by 51
“Other phylogenomic studies have also found high rates of gene tree discordance (Degnan and Rosenberg 2009; Wickett et al. 2014; Copetti et al. 2017; Pease et al. 2018; Liu et al. 2019).”
Self-citationJoining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits
Shah, T., Schneider, J. V., Zizka, G., Maurin, O., Baker, W. J., Forest, F., Brewer, G. E., Savolainen, V., Darbyshire, I., & Larridon, I. (2021) · American Journal of Botany · doi:10.1002/ajb2.1682 · Cited by 50
Timilsena, P. R., Wafula, E. K., Barrett, C. F., Ayyampalayam, S., McNeal, J. R., Rentsch, J. D., McKain, M. R., Heyduk, K., Harkess, A., Villegente, M., et al. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.876779 · Cited by 49
“Following methods used by the One Thousand Plant Transcriptome Initiative (Matasci et al. 2014; Wickett et al., 2014; OTPT Initiative, 2019), and implemented through the AssemblyPostProcessor steps in the PlantTribes toolkit (https:// github.com/dePamphilis/PlantTribes), if multiple transcript assemblies from a single…”
MethodSelf-citationRosato, M., Kovařı́k, A., Garilleti, R., & Rosselló, J. A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0162544 · Cited by 49
Mobile Elements Shape Plastome Evolution in Ferns
Robison, T. A., Grusz, A. L., Wolf, P. G., Mower, J. P., Fauskee, B. D., Sosa, K., & Schuettpelz, E. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy189 · Cited by 49
The Earth BioGenome project: opportunities and challenges for plant genomics and conservation
Expósito‐Alonso, M., Drost, H., Burbano, H. A., & Weigel, D. (2019) · The Plant Journal · doi:10.1111/tpj.14631 · Cited by 47
Ambrosino, L., Colantuono, C., Diretto, G., Fiore, A., & Chiusano, M. L. (2020) · Plants · doi:10.3390/plants9050591 · Cited by 49
Systems biology of resurrection plants
Gechev, T., Lyall, R., Petrov, V., & Bartels, D. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03913-8 · Cited by 48
Pichrtová, M., Holzinger, A., Kulichová, J., Ryšánek, D., Šoljaková, T., Trumhová, K., & Němcová, Y. (2018) · European Journal of Phycology · doi:10.1080/09670262.2018.1476920 · Cited by 48
“…an important research topic in current phycology, because conjugating green algae are considered to be the closest algal relatives of land plants (Wickett et al., 2014; Zhong et al., 2015), and the genetic identity of the vast majority of morphospecies is still unknown (however see e.g. Drummond…”
BackgroundDevos, N., Szövényi, P., Weston, D. J., Rothfels, C. J., Johnson, M. G., & Shaw, A. J. (2016) · New Phytologist · doi:10.1111/nph.13887 · Cited by 47
“140 141 The Sphagnopsida comprise one of four major speciose clades within the phylum 142 Bryophyta and it is an early diverging group within mosses (Goffinet & Shaw, 2009; 143 Chang & Graham, 2011; Wickett et al., 2014).”
BackgroundSelf-citationMarchantia: Past, Present and Future
Bowman, J. L., Araki, T., & Kohchi, T. (2016) · Plant and Cell Physiology · doi:10.1093/pcp/pcw023 · Cited by 48
“2006), but a recent analysis suggests that hornworts are the basal land plant lineage, with mosses and liverworts forming a sister clade to vascular plants (Wickett et al. 2014).”
Nonreciprocal complementation of KNOX gene function in land plants
Frangedakis, E., Saint‐Marcoux, D., Moody, L. A., Rabbinowitsch, E., & Langdale, J. A. (2016) · New Phytologist · doi:10.1111/nph.14318 · Cited by 48
“…at NCBI (http://ncbi.nlm.nih.gov), Phytozome (http://phytozome.jgi.doe. gov) and OneKP (http://bioinfodata.org/Blast4OneKP) (Johnson et al., 2012; Wickett et al., 2014; Xie et al., 2014), plus rice (http:// rice.plantbiology.msu.edu), Klebsormidium (http://www.plantmor…”
BackgroundEvolution of the plant body plan
Szövényi, P., Waller, M., & Kirbis, A. (2018) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2018.11.005 · Cited by 48
Pelosi, J. A., Kim, E. H., Barbazuk, W. B., & Sessa, E. B. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.882441 · Cited by 46
“Whole genome duplication, or polyploidy, is associated with nearly one-third of speciation events in ferns (Wood et al., 2009).”
BackgroundA transcriptomics investigation into pine reproductive organ development
Niu, S., Yuan, H., Sun, X., Porth, I. M., Li, Y., El-Kassaby, Y. A., & Li, W. (2015) · New Phytologist · doi:10.1111/nph.13680 · Cited by 47
Self-citationAn introduction to plant phylogenomics with a focus on palms
Barrett, C. F., Bacon, C. D., Antonelli, A., Cano, Á., & Hofmann, T. (2016) · Botanical Journal of the Linnean Society · doi:10.1111/boj.12399 · Cited by 46
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“This supports the hypothesis that the entire land plant lineage evolved from a single group within the CGA, namely the Zygnematophyceae (Wickett et al., 2014), which were able to colonize terrestrial habitats about 460 million years ago (Becker and Marin, 2009).”
Grewe, F., Huang, J.-P., Leavitt, S. D., & Lumbsch, H. T. (2017) · Scientific Reports · doi:10.1038/s41598-017-09906-7 · Cited by 47
Sussmilch, F. C., & McAdam, S. A. M. (2017) · Plants · doi:10.3390/plants6040054 · Cited by 48
“The relative timing of appearance of key traits is indicated on the current, most parsimonious phylogeny for land plants (not drawn to scale) that recognizes current uncertainty in the relationships between bryophytes (B) and vascular plants [161].”
BackgroundOrder‐level fern plastome phylogenomics: new insights from Hymenophyllales
Kuo, L., Qi, X., Mā, H., & Li, F. (2018) · American Journal of Botany · doi:10.1002/ajb2.1152 · Cited by 47
The promise and pitfalls of synteny in phylogenomics
Steenwyk, J. L., & King, N. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002632 · Cited by 49
Vajda, V., Pučetaitė, M., McLoughlin, S., Engdahl, A., Heimdal, J., & Uvdal, P. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0224-5 · Cited by 46
Metadata
- Authors
- Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., Ruhfel, B. R., Wafula, E., Der, J. P., Graham, S. W., Mathews, S., Melkonian, M., Soltis, D. E., Soltis, P. S., Miles, N. W., Rothfels, C. J., Pokorny, L., Shaw, A. J., DeGironimo, L., Stevenson, D. W., Surek, B., Villarreal, J. C., Roure, B., Philippe, H., dePamphilis, C. W., Chen, T., Deyholos, M. K., Baucom, R. S., Kutchan, T. M., Augustin, M. M., Wang, J., Zhang, Y., Tian, Z., Yan, Z., Wu, X., Sun, X., Wong, G. K.-S., & Leebens-Mack, J.
- Affiliations
- Northwestern University (US)
- The University of Texas at Austin (US)
- University of Alberta (CA)
- University of Arizona (US)
- University of Georgia (US)
- Department of Biology and
- University of Florida (US)
- Eastern Kentucky University (US)
- Pennsylvania State University (US)
- Department of Botany and
- Harvard University (US)
- University of Cologne (DE)
- Florida Museum of Natural History (US)
- University of British Columbia (CA)
- Consejo Superior de Investigaciones Científicas (ES)
- Duke University (US)
- New York Botanical Garden (US)
- Ludwig-Maximilians-Universität München (DE)
- Université de Montréal (CA)
- Centre National de la Recherche Scientifique (FR)
- Chinese Academy of Sciences (CN)
- University of Michigan (US)
- Donald Danforth Plant Science Center (US)
- BGI Group (China) (CN)
- Department of Plant Biology, University of Georgia, Athens, GA 30602;
- ORCID
- Wickett, Norman J.
- Mirarab, Siavash
- Nguyen, Nam
- Warnow, Tandy
- Carpenter, Eric
- Matasci, Naim
- Barker, Michael S.
- Burleigh, J. Gordon
- Gitzendanner, Matthew A.
- Ruhfel, Brad R.
- Wafula, Eric
- Der, Joshua P.
- Graham, Sean W.
- Mathews, Sarah
- Melkonian, Michael
- Rothfels, Carl J.
- Pokorny, Lisa
- Shaw, A. Jonathan
- Stevenson, Dennis W.
- Villarreal, Juan Carlos
- Philippe, Hervé
- dePamphilis, Claude W.
- Chen, Tao
- Deyholos, Michael K.
- Baucom, Regina S.
- Kutchan, Toni M.
- Augustin, Megan M.
- Wang, Jun
- Zhang, Yong
- Yan, Zhixiang
- Wu, Xiaolei
- Sun, Xiao
- Wong, Gane Ka-Shu
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2014-10-29
- Volume
- 111
- Issue
- 45
- Pages
- E4859-68
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4234587
- OpenAlex
- W2013277649
- Cited by
- 1,252
- References
- 124
- Citations by year
- 2026: 33 · 2025: 56 · 2024: 92 · 2023: 73 · 2022: 98 · 2021: 144 · 2020: 125 · 2019: 139 · 2018: 168 · 2017: 124 · 2016: 116 · 2015: 81 · 2014: 2
- FWCI
- 44.12
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (acceptedVersion)
- Civil War Book Review (submittedVersion)
- HAL (submittedVersion)
- Funders
- National Institute on Drug Abuse (R01DA025197)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- land plant origin, Zygnematophyceae, liverworts, bryophytes, plant phylogeny, nuclear gene phylogeny, phylogenetic robustness, coalescent phylogenetics, supertree, supermatrix
- MeSH terms
- Phylogeny, Sequence Alignment, DNA, Plant, Genome, Plant, Evolution, Molecular, Quantitative Trait, Heritable, Gene Expression Profiling, Streptophyta, Transcriptome
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