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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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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
Algorithm AS 136: A K-Means Clustering Algorithm
Hartigan, J. A., & Wong, M. A. (1979) · Applied Statistics · doi:10.2307/2346830 · Cited by 14,523
The Angiosperm Phylogeny Group (2016) · Botanical Journal of the Linnean Society · doi:10.1111/boj.12385 · Cited by 9,583
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 7,003
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
TNT, a free program for phylogenetic analysis
Goloboff, P. A., Farris, J. S., & Nixon, K. C. (2008) · Cladistics · doi:10.1111/j.1096-0031.2008.00217.x · Cited by 5,352
THE ANGIOSPERM PHYLOGENY GROUP (2009) · Botanical Journal of the Linnean Society · doi:10.1111/j.1095-8339.2009.00996.x · Cited by 4,911
Apg (2009) · Botanical Journal of the Linnean Society · Cited by 3,627
Research works printed but not linked: 4
- M Melkonian, B Surek, Phylogeny of the Chlorophyta—Congruence between ultrastructural and molecular evidence. Bulletin De La Societe Zoologique De France-Evolution Et Zoologie 120, 191–208 (1995).
- RE Timme, CF Delwiche, Phylogenomic reconstruction of the Charophytes: A multilocus approach to resolving the phylogeny of plants’ closest relatives. J Phycol 47, 16 (2011).
- JD Pickett-Heaps, The evoltuion of mitotic apparatus—An attempt at comparative ultrastructural cytology in dividing plant cells. Cytobios 1, 257–280 (1969).
- WR Philipson, A new approach to the origins of vascular plants. Botanische Jahrbucher 113, 443–460 (1991).
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“In a broad evolutionary context, a particularly interesting taxonomic group are streptophyte algae (Zygnematophyceae, Coleochaetophyceae, Charophyceae, and Klebsormidiophyceae), as they comprise the lineage in which the embryophytes evolved.”
BackgroundThe draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms
Dong, S., Chen, L., Liu, Y., Wang, Y., Zhang, S., Yang, L., Lang, X., & Zhang, S. (2020) · PLoS ONE · doi:10.1371/journal.pone.0231020 · Cited by 90
“Specifically, magnoliids (with Cinnamomum kanehirae as the only representative) is resolved as the sister to eudicots with relatively strong support [32], which is consistent with the result of the phylotranscriptomic analysis of the 1–kp data [34] and of 20 representative transcriptomes [35].”
InfluentialShen, X., Salichos, L., & Rokas, A. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw179 · Cited by 85
Gerke, P., Szövényi, P., Neubauer, A., Lenz, H., Gutmann, B., McDowell, R., Small, I., Schallenberg‐Rüdinger, M., & Knoop, V. (2019) · New Phytologist · doi:10.1111/nph.16297 · Cited by 89
“The discussion has recently been reactivated with analyses of large nuclear transcriptome data sets (Wickett et al., 2014; Cox, 2018; de Sousa et al., 2018; Morris et al., 2018; Puttick et al., 2018; Rensing, 2018a,b), questioning the previously suggested phylogeny with liverworts sister to all…”
BackgroundIs Phylotranscriptomics as Reliable as Phylogenomics?
Cheon, S., Zhang, J., & Park, C. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa181 · Cited by 89
“…relationships of diverse lineages of organisms (Hittinger et al. 2010; Kocot et al. 2011; Smith et al. 2011; Struck et al. 2011; Johnson et al. 2013; Riesgo et al. 2014; Wickett et al. 2014; Zeng et al. 2014; Irisarri et al. 2017; Janou (cid:2) skovec et al. 2017; Price Dana and Bhattacharya 2017).”
Baker, W. J., Dodsworth, S., Forest, F., Graham, S. W., Johnson, M. G., McDonnell, A., Pokorny, L., Tate, J. A., Wicke, S., & Wickett, N. J. (2021) · American Journal of Botany · doi:10.1002/ajb2.1703 · Cited by 89
“The One Thousand Plant Transcriptomes (1KP) initiative (Wickett et al., 2014; One Thousand Plant Transcriptomes Initiative, 2019) has been especially influential in addressing phylogenetic questions with nuclear genome-scale data, as it has placed hundreds of green plant transcriptomes in the…”
BackgroundSelf-citationSaint‐Marcoux, D., Proust, H., Dolan, L., & Langdale, J. A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0118678 · Cited by 89
“Although the phylogenetic relationship between the bryophyte lineages of liverworts, mosses and hornworts is still debated, the position of liverworts as one of (if not) the earliest land plant lineage(s) is undisputed [8].”
BackgroundPlant-specific CC-type glutaredoxins: functions in developmental processes and stress responses
Gutsche, N., Thurow, C., Zachgo, S., & Gatz, C. (2015) · Biological Chemistry · doi:10.1515/hsz-2014-0300 · Cited by 89
Tam, T. H. Y., Catarino, B., & Dolan, L. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416324112 · Cited by 88
Acquiring Control: The Evolution of Stomatal Signalling Pathways
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A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens
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Self-citationCrossroads in the evolution of plant specialized metabolism
Rieseberg, T. P., Dadras, A., Fürst‐Jansen, J. M. R., Ashok, A. D., Darienko, T., de Vries, S., Irisarri, I., & de Vries, J. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.03.004 · Cited by 88
ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization
Yin, J., Zhang, C., & Mirarab, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz211 · Cited by 80
Self-citationFerns: the missing link in shoot evolution and development
Plackett, A. R. G., Stilio, V. S. D., & Langdale, J. A. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.00972 · Cited by 85
“That said, Frontiers in Plant Science | www.frontiersin.org 3 November 2015 | Volume 6 | Article 972 the monilophytes themselves represent an ancient and highly diverse lineage, diverging from the seed plants 400 million years ago (Pryer et al., 2001) and encompassing a wide variety of growth…”
BackgroundMinimum variance rooting of phylogenetic trees and implications for species tree reconstruction
Mai, U., Sayyari, E., & Mirarab, S. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182238 · Cited by 87
Self-citationEvolutionary dynamics of mycorrhizal symbiosis in land plant diversification
Feijen, F. A. A., Vos, R. A., Nuytinck, J., & Merckx, V. S. F. T. (2018) · Scientific Reports · doi:10.1038/s41598-018-28920-x · Cited by 85
The performance of coalescent-based species tree estimation methods under models of missing data
Nute, M., Chou, J., Molloy, E. K., & Warnow, T. J. (2018) · BMC Genomics · doi:10.1186/s12864-018-4619-8 · Cited by 86
“, the plant transcriptome dataset studied in [19], the landfowl ultra-conserved elements (UCE) dataset studied in [20], and the iguanian lizard UCE dataset studied in [21]), where many genes are not present for some species (and so are “incomplete”).”
BackgroundSelf-citationLibertı́n, M., Kvaček, J., Bek, J., Žárský, V., & Štorch, P. (2018) · Nature Plants · doi:10.1038/s41477-018-0140-y · Cited by 86
de Vries, J., de Vries, S., Curtis, B. A., Zhou, H., Penny, S. L., Feussner, K., Pinto, D. M., Steinert, M., Cohen, A., von Schwartzenberg, K., et al. (2020) · The Plant Journal · doi:10.1111/tpj.14782 · Cited by 86
“(MZCH240) and Spirogyra pratensis (MZCH10213); these two species span some of the deepest branches of the phylogeny of Zygnematophyceae (Gontcharov and Melkonian, 2010; Wickett et al., 2014; Leebens-Mack et al., 2019).”
BackgroundMethodInfluentialEthylene-independent functions of the ethylene precursor ACC in Marchantia polymorpha
Li, D., Flores‐Sandoval, E., Ahtesham, U., Coleman, A., Clay, J. M., Bowman, J. L., & Chang, C. (2020) · Nature Plants · doi:10.1038/s41477-020-00784-y · Cited by 82
Koenen, E. J. M., Kidner, C. A., Souza, É. R. D., Simon, M. F., Iganci, J. R. V., Nicholls, J. A., Brown, G. K., de Queiroz, L. P., Luckow, M., Lewis, G. P., et al. (2020) · American Journal of Botany · doi:10.1002/ajb2.1568 · Cited by 89
“While those early studies used just a single locus, the plastid gene rbcL, modern studies often employ hundreds to several thousands of genes to infer phylogenetic relationships (e.g., Lee et al., 2011; Wen et al., 2013; Wickett et al., 2014; Yang et al., 2015; Zeng et al., 2017).”
BackgroundA target enrichment probe set for resolving the flagellate land plant tree of life
Breinholt, J. W., Carey, S. B., Tiley, G. P., Davis, E., Endara, L., McDaniel, S. F., Neves, L. G., Sessa, E. B., von Konrat, M., Chantanaorrapint, S., et al. (2021) · Applications in Plant Sciences · doi:10.1002/aps3.11406 · Cited by 86
Self-citationDeep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies
Suvorov, A., Scornavacca, C., Fujimoto, M., Bodily, P., Clement, M., Crandall, K. A., Whiting, M. F., Schrider, D. R., & Bybee, S. (2021) · Systematic Biology · doi:10.1093/sysbio/syab063 · Cited by 97
“Also, since fragmentary data may have a negative effect on accuracy of gene and hence species tree inference (Wickett et al. 2014), sequence fragments with >50% gap characters were removed from clusters that were used to estimate trees with ASTRAL v4.”
MethodPhytohormone Profiling across the Bryophytes
Drábková, L. Z., Dobrev, P. I., & Motyka, V. (2015) · PLoS ONE · doi:10.1371/journal.pone.0125411 · Cited by 86
“Among bryophytes, the liverworts are the earliest lineage sister to all other groups of land plants [47].”
BackgroundReconstructing trait evolution in plant evo–devo studies
Delaux, P., Hetherington, A. J., Coudert, Y., Delwiche, C. F., Dunand, C., Gould, S. B., Kenrick, P., Li, F., Philippe, H., Rensing, S. A., et al. (2019) · Current Biology · doi:10.1016/j.cub.2019.09.044 · Cited by 85
Self-citationOn the importance of homology in the age of phylogenomics
Springer, M. S., & Gatesy, J. (2017) · Systematics and Biodiversity · doi:10.1080/14772000.2017.1401016 · Cited by 83
Multispecies Coalescent: Theory and Applications in Phylogenetics
Mirarab, S., Nakhleh, L. K., & Warnow, T. J. (2021) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-012121-095340 · Cited by 85
Self-citationDIX Domain Polymerization Drives Assembly of Plant Cell Polarity Complexes
van Dop, M., Fiedler, M., Mutte, S. K., de Keijzer, J., Olijslager, L. H., Albrecht, C., Liao, C., Janson, M. E., Bienz, M., & Weijers, D. (2020) · Cell · doi:10.1016/j.cell.2020.01.011 · Cited by 87
“To identity other SOSEKI proteins in the plant kingdom, we searched the OneKP dataset (Matasci et al., 2014; Wickett et al., 2014) using a bioinformatic pipeline as previously described (Mutte et al.”
BackgroundMethodMedina, R., Johnson, M. G., Liu, Y., Wickett, N. J., Shaw, A. J., & Goffinet, B. (2019) · Journal of Systematics and Evolution · doi:10.1111/jse.12516 · Cited by 83
Self-citationGenomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life
Hao, D., & Xiao, P. (2015) · Evolutionary Bioinformatics · doi:10.4137/ebo.s31326 · Cited by 83
Wang, Y., Qu, X., Chen, S., Li, D.-Z., & Yi, T. (2017) · Tree Genetics & Genomes · doi:10.1007/s11295-017-1124-1 · Cited by 82
Simmons, M. P., & Gatesy, J. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.05.011 · Cited by 84
“Furthermore, the greater robustness of ASTRAL is consistent with the best supported resolution of Amborella based on our other analyses described above as well as other recent phylogenomic analyses (Drew et al., 2014; Ruhfel et al., 2014; Wickett et al., 2014).”
BackgroundMethodResultInfluentialLarson, D. A., Walker, J. F., Vargas, O. M., & Smith, S. A. (2020) · American Journal of Botany · doi:10.1002/ajb2.1469 · Cited by 78
The origin and evolution of phototropins
Li, F., Rothfels, C. J., Melkonian, M., Villarreal, J. C., Stevenson, D. W., Graham, S. W., Wong, G. K., Mathews, S., & Pryer, K. M. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.00637 · Cited by 85
“Our phototropin phylogeny is largely congruent with published organismal relationships (Forrest et al., 2006; Cox et al., 2010; Gontcharov and Melkonian, 2010; Villarreal and Renner, 2012; Wickett et al., 2014; Rothfels et al., 2015).”
BackgroundMethodInfluentialSelf-citationHigo, A., Kawashima, T., Borg, M., Zhao, M., López‐Vidriero, I., Sakayama, H., Montgomery, S. A., Sekimoto, H., Hackenberg, D., Shimamura, M., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07728-3 · Cited by 82
Gatesy, J., Meredith, R. W., Janečka, J. E., Simmons, M. P., Murphy, W. J., & Springer, M. S. (2016) · Cladistics · doi:10.1111/cla.12170 · Cited by 81
Why we need more non‐seed plant models
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Wu, M., Kostyun, J. L., Hahn, M. W., & Moyle, L. C. (2018) · Molecular Ecology · doi:10.1111/mec.14780 · Cited by 81
Environmental gradients reveal stress hubs pre-dating plant terrestrialization
Dadras, A., Fürst‐Jansen, J. M. R., Darienko, T., Krone, D., Scholz, P., Sun, S., Herrfurth, C., Rieseberg, T. P., Irisarri, I., Steinkamp, R., et al. (2023) · Nature Plants · doi:10.1038/s41477-023-01491-0 · Cited by 86
“patens: SRR1824306 to SRR1824320, SRR10235460 to SRR10235483, SRR787291, SRR787292, SRR787293, SRR787294, SRR787295; (4) Z.”
What are the evolutionary origins of stomatal responses to abscisic acid in land plants?
Sussmilch, F. C., Brodribb, T. J., & McAdam, S. A. M. (2017) · Journal of Integrative Plant Biology · doi:10.1111/jipb.12523 · Cited by 82
Why Are There So Many Flowering Plants? A Multiscale Analysis of Plant Diversification
Hernández‐Hernández, T., & Wiens, J. J. (2020) · The American Naturalist · doi:10.1086/708273 · Cited by 80
“The topology is broadly congruent with more recent studies having more extensive gene sampling but more limited taxon sampling (e.g., Wickett et al. 2014; APGIII 2016).”
ResultPlant evolution and terrestrialization during Palaeozoic times - the phylogenetic context
Gerrienne, P., Servais, T., & Vecoli, M. (2016) · Review of Palaeobotany and Palynology · doi:10.1016/j.revpalbo.2016.01.004 · Cited by 80
Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic EstimatesPreprint
Buddenhagen, C. E., Lemmon, A. R., Lemmon, E. M., Bruhl, J. J., Cappa, J. J., Clement, W. L., Donoghue, M. J., Edwards, E. J., Hipp, A. L., Kortyna, M., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/086298 · Cited by 84
“When the loci being modeled are from protein coding regions, some authors choose to partition by codon position and remove third codon positions in order to reduce the effects of substitutional saturation (e.g., Breinholt and Kawahara 2013; Wickett et al. 2014; Frandsen et al. 2015).”
BackgroundResultInfluentialSelf-citationOccurrence of brassinosteroids in non-flowering land plants, liverwort, moss, lycophyte and fern
Yokota, T., Ohnishi, T., Shibata, K., Asahina, M., Nomura, T., Fujita, T., Ishizaki, K., & Kohchi, T. (2017) · Phytochemistry · doi:10.1016/j.phytochem.2016.12.020 · Cited by 79
Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life
Kulkarni, S., Kallal, R. J., Wood, H. M., Dimitrov, D., Giribet, G., & Hormiga, G. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa251 · Cited by 80
What is the age of flowering plants?
Sauquet, H., Ramírez‐Barahona, S., & Magallón, S. (2022) · Journal of Experimental Botany · doi:10.1093/jxb/erac130 · Cited by 79
Davidson, R., Vachaspati, P., Mirarab, S., & Warnow, T. J. (2015) · BMC Genomics · doi:10.1186/1471-2164-16-s10-s1 · Cited by 79
Self-citationLemieux, C., Otis, C., & Turmel, M. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.00697 · Cited by 65
“…et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada The Streptophyta comprises all land plants and six main lineages of freshwater green algae: Mesostigmatophyceae, Chlorokybophyceae, Klebsormidiophyceae, Charophyceae,…”
BackgroundResultInfluentialChomicki, G., Coiro, M., & Renner, S. S. (2017) · Annals of Botany · doi:10.1093/aob/mcx113 · Cited by 83
Field-based species identification of closely-related plants using real-time nanopore sequencing
Parker, J., Helmstetter, A. J., Devey, D. S., Wilkinson, T., & Papadopulos, A. S. T. (2017) · Scientific Reports · doi:10.1038/s41598-017-08461-5 · Cited by 80
“These predicted gene sequences were combined with a published dataset spanning 852 orthologous, single-copy genes 28 , downsam-pled to 6 representative taxa.”
BackgroundMethodInfluentialChloroplast phylogenomics resolves key relationships in ferns
Lu, J.-M., Zhang, N., Du, X., Wen, J., & Li, D.-Z. (2015) · Journal of Systematics and Evolution · doi:10.1111/jse.12180 · Cited by 75
Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes
Johnson, K. L., Cassin, A. M., Lonsdale, A., Wong, G. K., Soltis, P. S., Miles, N. W., Melkonian, M., Melkonian, B., Deyholos, M. K., Leebens‐Mack, J., et al. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.00295 · Cited by 78
Self-citationRevisiting the Great Ordovician Diversification of land plants: Recent data and perspectives
Servais, T., Cascales-Miñana, B., Cleal, C. J., Gerrienne, P., Harper, D. A. T., & Neumann, M. (2019) · Palaeogeography, Palaeoclimatology, Palaeoecology · doi:10.1016/j.palaeo.2019.109280 · Cited by 77
Gao, B., Li, X., Zhang, D., Liang, Y., Yang, H., Chen, M., Zhang, Y., Zhang, J., & Wood, A. J. (2017) · Scientific Reports · doi:10.1038/s41598-017-07297-3 · Cited by 77
Self-citationIbanez, S. G., Zamarreño, A. M., García‐Mina, J. M., & Solano, R. (2019) · Current Biology · doi:10.1016/j.cub.2019.05.079 · Cited by 71
Plant genomes: Markers of evolutionary history and drivers of evolutionary change
Soltis, P. S., & Soltis, D. E. (2020) · Plants People Planet · doi:10.1002/ppp3.10159 · Cited by 76
Self-citationJensen, J., Busse-Wicher, M., Poulsen, C., Fangel, J., Smith, P. J., Yang, J.-Y., Pena, M., Dinesen, M., Martens, H., Melkonian, M., et al. (2018) · New Phytologist · doi:10.1111/nph.15050 · Cited by 65
“1) have been proposed as the closest extant relatives (Wickett et al., 2014).”
BackgroundSelf-citationJohnson, M. G., Pokorny, L., Dodsworth, S., Botigué, L. R., Cowan, R. S., Devault, A. M., Eiserhardt, W. L., Epitawalage, N., Forest, F., Kim, J. T., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/361618 · Cited by 77
Self-citationThe Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves
Evkaikina, A. I., Berke, L., Андреевна, Р. М., Proux‐Wéra, E., Ivanova, A. N., Rydin, C., Pawlowski, K., & Voitsekhovskaja, O. V. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx169 · Cited by 393
“…the Lycopodiophyta, transcriptome data sets for species that contained both class I and class II KNOX transcripts were obtained from the OneKP database, namely, Lycopodium deuterodensum, Isoetes tegetiformans, Selaginella apoda, and Selaginella kraussiana (Matasci et al. 2014; Wickett et al. 2014).”
MethodPhylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants
Smith, S. A., Walker‐Hale, N., Walker, J. F., & Brown, J. W. (2019) · Systematic Biology · doi:10.1093/sysbio/syz078 · Cited by 75
Evolution of nuclear auxin signaling: lessons from genetic studies with basal land plants
Kato, H., Nishihama, R., Weijers, D., & Kohchi, T. (2017) · Journal of Experimental Botany · doi:10.1093/jxb/erx267 · Cited by 71
“Land plants evolved from aquatic green algae consisting of two groups: 75 chlorophytes and charophytes, the latter of which forms a sister group of land 76 plants (Bowman, 2013; Wickett et al., 2014).”
BackgroundNie, Y., Foster, C. S. P., Zhu, T., Yao, R., Duchêne, D. A., Ho, S. Y. W., & Zhong, B. (2019) · Systematic Biology · doi:10.1093/sysbio/syz032 · Cited by 72
RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs
Yaari, R., Katz, A., Domb, K., Harris, K. D., Zemach, A., & Ohad, N. (2019) · Nature Communications · doi:10.1038/s41467-019-09496-0 · Cited by 74
Dong, S., Liu, M., Liu, Y., Chen, F., Yang, T., Chen, L., Zhang, X., Guo, X., Fang, D., Li, L., et al. (2021) · Horticulture Research · doi:10.1038/s41438-021-00471-9 · Cited by 74
Decoding ABA and osmostress signalling in plants from an evolutionary point of view
Komatsu, K., Takezawa, D., & Sakata, Y. (2020) · Plant Cell & Environment · doi:10.1111/pce.13869 · Cited by 76
Challenging the paradigms of leaf evolution: Class III HD‐Zips in ferns and lycophytes
Vasco, A., Smalls, T. L., Graham, S. W., Cooper, E. D., Wong, G. K., Stevenson, D. W., Moran, R. C., & Ambrose, B. A. (2016) · New Phytologist · doi:10.1111/nph.14075 · Cited by 72
“Recent molecular phylogenies place Equisetum as sister to all ferns (Rai & Graham, 2010; Wickett et al., 2014; Knie et al., 2015; Rothfels et al., 2015), a position that is more in agreement with the morphological analyses that include fossils (Rothwell, 1999; Rothwell & Nixon, 2006).”
ResultSelf-citationLyczakowski, J. J., Wicher, K., Terrett, O. M., Faria-Blanc, N., Yu, X.-L., Brown, D. M., Krogh, K. B. R. M., Dupree, P., & Busse-Wicher, M. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-017-0902-1 · Cited by 79
“The same Arabidopsis CDSs were used as a query to identify transcripts encoding putative GUX enzymes from Coniferophyta and Gnetophyta transcriptomic data available via 1000 Plant Genome BLAST service [26].”
MethodEstablishment of Anthoceros agrestis as a model species for studying the biology of hornworts
Szövényi, P., Frangedakis, E., Ricca, M., Quandt, D., Wicke, S., & Langdale, J. A. (2015) · BMC Plant Biology · doi:10.1186/s12870-015-0481-x · Cited by 71
“Moreover, the data supported monophyly of liverworts and mosses, a relationship that is further validated by phylotranscriptomic analyses of a much larger taxon group [9].”
BackgroundChloroplast Phylogenomic Inference of Green Algae Relationships
Sun, L., Fang, L., Zhang, Z., Chang, X., Penny, D., & Zhong, B. (2016) · Scientific Reports · doi:10.1038/srep20528 · Cited by 71
Soriano, G., Cloix, C., Heilmann, M., Núñez‐Olivera, E., Martínez‐Abaigar, J., & Jenkins, G. I. (2017) · New Phytologist · doi:10.1111/nph.14767 · Cited by 71
“Yet, the fossil record and molecular phylogenies have not definitively clarified the evolutionary sequence of the three bryophyte lineages (Qiu et al., 2007; Liu et al., 2014; Wickett et al., 2014; Bowman et al., 2016).”
BackgroundTelomerase RNAs in land plants
Fajkus, P., Peška, V., Závodník, M., Fojtová, M., Fulnečková, J., Dobias, Š., Kilar, A., Dvořáčková, M., Zachová, D., Nečasová, I., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz695 · Cited by 71
Ties between Stress and Lipid Droplets Pre-date Seeds
de Vries, J., & Ischebeck, T. (2020) · Trends in Plant Science · doi:10.1016/j.tplants.2020.07.017 · Cited by 70
Genome‐scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets
Hu, H., Sun, P., Yang, Y. P., Ma, J., & Liu, J. (2023) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13455 · Cited by 70
Tracheophyte genomes keep track of the deep evolution of the Caulimoviridae
Diop, S. I., Geering, A. D. W., Alfama, F., Loaec, M., Teycheney, P., & Maumus, F. (2018) · Scientific Reports · doi:10.1038/s41598-017-16399-x · Cited by 70
Charting the genomic landscape of seed-free plants
Szövényi, P., Gunadi, A., & Li, F. (2021) · Nature Plants · doi:10.1038/s41477-021-00888-z · Cited by 69
Evolutionary Significance of NHX Family and NHX1 in Salinity Stress Adaptation in the Genus Oryza
Solis, C. A., Yong, M., Zhou, M., Venkataraman, G., Shabala, L., Holford, P., Shabala, S. N., & Chen, Z. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23042092 · Cited by 69
“We surveyed and selected representative species that are phylogenetically important in land plant evolution [44,45].”
BackgroundA Practical Guide to Design and Assess a Phylogenomic Study
Lozano-Fernández, J. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac129 · Cited by 73
“Some simulation studies concluded that their impact is small in large datasets, up to levels of missing data of 50% (Wiens and Morrill 2011), and empirical studies with similar levels have been proved to not bias the resulting topology at least in some lineages (e.g., Fernández et al. 2014, 2016).”
BackgroundPhylogenomic inference in extremis: A case study with mycoheterotroph plastomes
Lam, V. K. Y., Darby, H., Merckx, V. S. F. T., LIM, G. S., Yukawa, T., Neubig, K. M., Abbott, J. R., Beatty, G. E., Provan, J., Gomez, M. S., et al. (2018) · American Journal of Botany · doi:10.1002/ajb2.1070 · Cited by 68
Self-citationWróblewski, T., Spiridon, L. N., Martin, E. C., Petrescu, A., Cavanaugh, K., Truco, M. J., Xu, H., Gozdowskı, D., Pawłowski, K., Michelmore, R. W., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2005821 · Cited by 68
“Canonical NLRs evolve rapidly, being highly diverse across different taxa, yet despite approximately 100 million years following the separation of superrosid (Arabidopsis) and superasterid (lettuce) lineages [60], the identified NLR pair retained a functional relationship.”
BackgroundPlackett, A. R. G., Conway, S. J., Hazelton, K. D. H., Rabbinowitsch, E., Langdale, J. A., & Stilio, V. S. D. (2018) · eLife · doi:10.7554/elife.39625 · Cited by 68
Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model
Liu, L., Anderson, C. N. K., Pearl, D. K., & Edwards, S. V. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9074-0_7 · Cited by 68
TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution
Zhang, C., Zhao, Y., Braun, E. L., & Mirarab, S. (2021) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13696 · Cited by 72
Self-citationThe monoplastidic bottleneck in algae and plant evolution
de Vries, J., & Gould, S. B. (2017) · Journal of Cell Science · doi:10.1242/jcs.203414 · Cited by 70
“2; cf. Vaughn et al., 1992) and usually branch at the base of the primarily polyplastidic land plants (Wickett et al., 2014).”
BackgroundElgorriaga, A., Escapa, I. H., Rothwell, G. W., Tomescu, A. M. F., & Cúneo, N. R. (2018) · American Journal of Botany · doi:10.1002/ajb2.1125 · Cited by 68
Naramoto, S., Hata, Y., Fujita, T., & Kyozuka, J. (2021) · The Plant Cell · doi:10.1093/plcell/koab218 · Cited by 67
Iwasaki, M., Kajiwara, T., Yasui, Y., Yoshitake, Y., Miyazaki, M., Kawamura, S., Suetsugu, N., Nishihama, R., Yamaoka, S., Wanke, D., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.10.023 · Cited by 67
Herburger, K., Xin, A., & Holzinger, A. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00540 · Cited by 66
“Zygnematophyceae, members of the charophyte green algae (CGA), are considered the sole ancestors of land plants (Wickett et al., 2014) and therefore must have evolved strategies to survive under terrestrial conditions.”
BackgroundDierschke, T., Flores‐Sandoval, E., Rast-Somssich, M. I., Althoff, F., Zachgo, S., & Bowman, J. L. (2021) · eLife · doi:10.7554/elife.57088 · Cited by 61
“patens (Genbank), from available transcriptomes (Wickett et al., 2014; Dong et al., 2019; Radhakrishnan et al., 2020), Klebsormidium and Caulerpa sequences derived from genome sequences (Hori et al.”
BackgroundTan, Q. W., Lim, P. K., Chen, Z., Pasha, A., Provart, N. J., Arend, M., Nikoloski, Z., & Mutwil, M. (2023) · Nature Communications · doi:10.1038/s41467-023-36517-w · Cited by 66
“We then defined the edges as expected if: (1) TFA (up-/down-regulated, activator) regulates TFB (up-/down-regulated), (2) TFA (down-/upregulated, repressor) regulates TFB (up-/down-regulated).”
Pipeline to Identify Hydroxyproline-Rich Glycoproteins
Johnson, K. L., Cassin, A. M., Lonsdale, A., Bacic, A., Doblin, M. S., & Schultz, C. J. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.00294 · Cited by 68
“The 1KP project (www. onekp.com) was established to allow researchers to more effectively address evolutionary and other questions by providing deeper sampling of key plant taxa beyond those with sequenced genomes (Johnson et al., 2012; Matasci et al., 2014; Wickett et al., 2014; Xie et al., 2014).”
BackgroundOn plant defense signaling networks and early land plant evolution
de Vries, S., de Vries, J., von Dahlen, J. K., Gould, S. B., Archibald, J. M., Rose, L. E., & Slamovits, C. H. (2018) · Communicative & Integrative Biology · doi:10.1080/19420889.2018.1486168 · Cited by 65
“from streptophyte algae (the closest extant relatives to land plants [3-5]), mosses, gymnosperms, and angiosperms.”
BackgroundMathew, I. E., & Agarwal, P. (2018) · BioEssays · doi:10.1002/bies.201800018 · Cited by 65
Impact of sequencing depth and technology on de novo RNA-Seq assembly
Patterson, J., Carpenter, E. J., Zhu, Z., An, D., Liang, X., Geng, C., Drmanac, R., & Wong, G. K. (2019) · BMC Genomics · doi:10.1186/s12864-019-5965-x · Cited by 70
Self-citationBell, D., Lin, Q., Gerelle, W. K., Joya, S., Chang, Y., Taylor, Z. N., Rothfels, C. J., Larsson, A. O., Villarreal, J. C., Li, F., et al. (2019) · American Journal of Botany · doi:10.1002/ajb2.1397 · Cited by 65
“A growing body of phylogenetic evidence from morphological and molecular studies now supports the view that extant bryophytes comprise three distinct branches of land plants, with extant vascular plants (tracheophytes) representing the fourth major land-plant lineage (Mishler and Churchill, 1984; Mishler et al., 1994;…”
BackgroundMethodResultInfluentialSelf-citationWater lilies as emerging models for Darwin’s abominable mystery
Chen, F., Liu, X., Yu, C., Chen, Y., Tang, H., & Zhang, L. (2017) · Horticulture Research · doi:10.1038/hortres.2017.51 · Cited by 70
Cai, S., Huang, Y., Chen, F., Zhang, X., Sessa, E. B., Zhao, C., Marchant, D. B., Xue, D., Chen, G. J., Dai, F., et al. (2020) · New Phytologist · doi:10.1111/nph.17135 · Cited by 65
“Plant photosynthesis is regulated by stomata, small pores on plant leaves and stems formed by guard cells (Willmer & Fricker, 1996).”
BackgroundSelf-citationPossart, A., Xu, T., Paik, I., Hanke, S. T., Keim, S., Hermann, H.-M., Wolf, L., Hiß, M., Becker, C., Huq, E., et al. (2017) · The Plant Cell · doi:10.1105/tpc.16.00388 · Cited by 65
From reproduction to production, stomata are the master regulators
Brodribb, T. J., Sussmilch, F. C., & McAdam, S. A. M. (2019) · The Plant Journal · doi:10.1111/tpj.14561 · Cited by 65
Wong, G. K., Soltis, P. S., Leebens‐Mack, J., Wickett, N. J., Barker, M. S., de Peer, Y. V., Graham, S. W., & Melkonian, M. (2019) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042916-041040 · Cited by 65
Self-citationPhylogenomic conflict coincides with rapid morphological innovation
Parins‐Fukuchi, C., Stull, G. W., & Smith, S. A. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2023058118 · Cited by 66
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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