Kenrick, P. & Crane, P. R. The origin and early evolution of plants on land. Nature 389, 33–39 (1997).
Bowman, J. L. The origin of a land flora. Nat. Plants 8, 1352–1369 (2022).
Graham, L. E., Cook, M. E. & Busse, J. S. The origin of plants: body plan changes contributing to a major evolutionary radiation. Proc. Natl Acad. Sci. USA 97, 4535–4540 (2000).
Puttick, M. N. et al. The interrelationships of land plants and the nature of the ancestral embryophyte. Curr. Biol. 28, 733–745 (2018).
Leebens-Mack, J. H. et al. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679–685 (2019).
Su, D. et al. Large-scale phylogenomic analyses reveal the monophyly of bryophytes and neoproterozoic origin of land plants. Mol. Biol. Evol. 38, 3332–3344 (2021).
Harris, B. J. et al. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat. Ecol. Evol. 6, 1634–1643 (2022).
Harris, B. J., Harrison, C. J., Hetherington, A. M. & Williams, T. A. Phylogenomic evidence for the monophyly of bryophytes and the reductive evolution of stomata. Curr. Biol. 30, 2001–2012 (2020).
Sousa, F., Foster, P. G., Donoghue, P. C. J., Schneider, H. & Cox, C. J. Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.). New Phytol. 222, 565–575 (2019).
Christenhusz, M. & Byng, J. The number of known plants species in the world and its annual increase. Phytotaxa 261, 201–217 (2016).
Degola, F., Sanità di Toppi, L. & Petraglia, A. Bryophytes: how to conquer an alien planet and live happily (ever after). J. Exp. Bot. 73, 4267–4272 (2022).
Ligrone, R., Duckett, J. G. & Renzaglia, K. S. Major transitions in the evolution of early land plants: a bryological perspective. Ann. Bot. 109, 851–871 (2012).
Shaw, J. & Renzaglia, K. Phylogeny and diversification of bryophytes. Am. J. Bot. 91, 1557–1581 (2004).
Glime, J. M. Primitive or advanced? Bryological 55, 5–7 (1990).
Bowman, J. L. et al. Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell 171, 287–304 (2017).
Rensing, S. A. et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319, 64–69 (2008).
Zhang, J. et al. The hornwort genome and early land plant evolution. Nat. Plants 6, 107–118 (2020).
Li, F. W. et al. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nat. Plants 6, 259–272 (2020).
Hu, R. et al. Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet. Cell 186, 3558–3576 (2023).
Marks, R. A., Hotaling, S., Frandsen, P. B. & VanBuren, R. Representation and participation across 20 years of plant genome sequencing. Nat. Plants 7, 1571–1578 (2021).
Szövényi, P., Gunadi, A. & Li, F. W. Charting the genomic landscape of seed-free plants. Nat. Plants 7, 554–565 (2021).
Renzaglia, K. S., Villarreal Aguilar, J. C. & Garbary, D. J. Morphology supports the setaphyte hypothesis: mosses plus liverworts form a natural group. Bryophyt. Divers. Evol. 40, 11–17 (2018).
Frangedakis, E. et al. The hornworts: morphology, evolution and development. New Phytol. 229, 735–754 (2021).
Liu, Y. et al. Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nat. Commun. 10, 1485 (2019).
Bowles, A. M. C., Bechtold, U. & Paps, J. The origin of land plants is rooted in two bursts of genomic novelty. Curr. Biol. 30, 530–536 (2020).
McElwain, J. C. & Punyasena, S. W. Mass extinction events and the plant fossil record. Trends Ecol. Evol. 22, 548–557 (2007).
Zhang, L. et al. Rapid evolution of protein diversity by de novo origination in Oryza. Nat. Ecol. Evol. 3, 679–690 (2019).
Cui, X. et al. Young genes out of the male: an insight from evolutionary age analysis of the pollen transcriptome. Mol. Plant 8, 935–945 (2015).
Wu, D. D. et al. ‘Out of pollen’ hypothesis for origin of new genes in flowering plants: study from Arabidopsis thaliana. Genome Biol. Evol. 6, 2822–2829 (2014).
Jin, G. et al. New genes interacted with recent whole-genome duplicates in the fast stem growth of bamboos. Mol. Biol. Evol. 38, 5752–5768 (2021).
Long, M., VanKuren, N. W., Chen, S. & Vibranovski, M. D. New gene evolution: little did we know. Annu. Rev. Genet. 47, 307–333 (2013).
Xu, X. et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 30, 105–111 (2011).
Villarreal, A. J., Crandall-Stotler, B. J., Hart, M. L., Long, D. G. & Forrest, L. L. Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate. New Phytol. 209, 1734–1746 (2016).
Linde, A. M., Eklund, D. M., Cronberg, N., Bowman, J. L. & Lagercrantz, U. Rates and patterns of molecular evolution in bryophyte genomes, with focus on complex thalloid liverworts, Marchantiopsida. Mol. Phylogenet. Evol. 165, 107295 (2021).
Carvunis, A. R. et al. Proto-genes and de novo gene birth. Nature 487, 370–374 (2012).
Xia, S., Chen, J., Arsala, D., Emerson, J. J. & Long, M. Functional innovation through new genes as a general evolutionary process. Nat. Genet. 57, 295–309 (2025).
Vuruputoor, V. S. et al. Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana. G3 (Bethesda) 14, jkae104 (2024).
Kolukisaoglu, Ü. D-amino acids in plants: sources, metabolism, and functions. Int. J. Mol. Sci. 21, 5421 (2020).
Yow, G.-Y., Uo, T., Yoshimura, T. & Esaki, N. Physiological role of d-amino acid-N-acetyltransferase of Saccharomyces cerevisiae: detoxification of d-amino acids. Arch. Microbiol. 185, 39–46 (2006).
Ludin, K. M., Hilti, N. & Schweingruber, M. E. Schizosaccharomyces pombe rds1, an adenine-repressible gene regulated by glucose, ammonium, phosphate, carbon dioxide and temperature. Mol. Gen. Genet 248, 439–445 (1995).
Sudmoon, R., Sattayasai, N., Bunyatratchata, W., Chaveerach, A. & Nuchadomrong, S. Thermostable mannose-binding lectin from Dendrobium findleyanum with activities dependent on sulfhydryl content. Acta Biochim. Biophys. Sin. (Shanghai) 40, 811–818 (2008).
Sattayasai, N. et al. Dendrobium findleyanum agglutinin: production, localization, anti-fungal activity and gene characterization. Plant Cell Rep. 28, 1243–1252 (2009).
Holm, D. K. et al. Molecular and chemical characterization of the biosynthesis of the 6-MSA-derived meroterpenoid yanuthone D in Aspergillus niger. Chem. Biol. 21, 519–529 (2014).
Ayers, S. et al. Noreupenifeldin, a tropolone from an unidentified ascomycete. J. Nat. Prod. 71, 457–459 (2008).
Romani, F. et al. Oil body formation in Marchantia polymorpha is controlled by MpC1HDZ and serves as a defense against arthropod herbivores. Curr. Biol. 30, 2815–2828 (2020).
Kanazawa, T. et al. The liverwort oil body is formed by redirection of the secretory pathway. Nat. Commun. 11, 6152 (2020).
Ma, J. et al. Major episodes of horizontal gene transfer drove the evolution of land plants. Mol. Plant 15, 857–871 (2022).
Wu, K., Guo, Y. & Head, G. Resistance monitoring of Helicoverpa armigera (Lepidoptera: Noctuidae) to bt insecticidal protein during 2001–2004 in China. J. Econ. Entomol. 99, 893–898 (2006).
Gage, M. J., Bruenn, J., Fischer, M., Sanders, D. & Smith, T. J. KP4 fungal toxin inhibits growth in Ustilago maydis by blocking calcium uptake. Mol. Microbiol. 41, 775–785 (2001).
Guan, Y. et al. Horizontally acquired fungal killer protein genes affect cell development in mosses. Plant J. 113, 665–676 (2023).
Sun, G. et al. Are fungi-derived genomic regions related to antagonism towards fungi in mosses? New Phytol. 228, 1169–1175 (2020).
Qiao, X. et al. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol. 20, 38 (2019).
McLysaght, A. & Hurst, L. D. Open questions in the study of de novo genes: what, how and why. Nat. Rev. Genet. 17, 567–578 (2016).
Kondrashov, A. S. & Crow, J. F. Haploidy or diploidy: which is better? Nature 351, 314–315 (1991).
Huang, J. Horizontal gene transfer in eukaryotes: the weak-link model. Bioessays 35, 868–875 (2013).
Dong, X. M. et al. Orphan gene PpARDT positively involved in drought tolerance potentially by enhancing ABA response in Physcomitrium (Physcomitrella) patens. Plant Sci. 319, 111222 (2022).
Liu, S. et al. The Antarctic moss Pohlia nutans genome provides insights into the evolution of bryophytes and the adaptation to extreme terrestrial habitats. Front. Plant Sci. 13, 920138 (2022).
Chen, F. et al. Terpenoid secondary metabolites in bryophytes: chemical diversity, biosynthesis and biological functions. Crit. Rev. Plant Sci. 37, 210–231 (2018).
Jia, Q., Kollner, T. G., Gershenzon, J. & Chen, F. MTPSLs: new terpene synthases in nonseed plants. Trends Plant Sci. 23, 121–128 (2018).
Xie, C. & Lou, H. Secondary metabolites in bryophytes: an ecological aspect. Chem. Biodivers. 6, 303–312 (2009).
Romani, F. et al. Liverwort oil bodies: diversity, biochemistry, and molecular cell biology of the earliest secretory structure of land plants. J. Exp. Bot. 73, 4427–4439 (2022).
Asakawa, Y., Ludwiczuk, A. & Nagashima, F. Chemical constituents of bryophytes. Bio- and chemical diversity, biological activity, and chemosystematics. Prog. Chem. Org. Nat. Prod. 95, 1–796 (2013).
Söderström, L. et al. World checklist of hornworts and liverworts. PhytoKeys 27, 1–828 (2016).
Urich, M. A., Nery, J. R., Lister, R., Schmitz, R. J. & Ecker, J. R. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat. Protoc. 10, 475–483 (2015).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Marcais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
Liu, B. et al. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome project. Preprint at arXiv https://doi.org/10.48550/arXiv.1308.2012 (2013).
Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202–2204 (2017).
Vaser, R., Sovic, I., Nagarajan, N. & Sikic, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 727–736 (2017).
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
Weisenfeld, N. I., Kumar, V., Shah, P., Church, D. M. & Jaffe, D. B. Direct determination of diploid genome sequences. Genome Res. 27, 757–767 (2017).
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).
Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99–101 (2016).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Edgar, R. C. & Myers, E. W. PILER: identification and classification of genomic repeats. Bioinformatics 21, i152–i158 (2005).
Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265–W268 (2007).
Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21, i351–i358 (2005).
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117, 9451–9457 (2020).
Jurka, J. et al. Repbase update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467 (2005).
McCarthy, E. M. & McDonald, J. F. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19, 362–367 (2003).
Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276–277 (2000).
Kamisugi, Y. et al. A sequence-anchored genetic linkage map for the moss, Physcomitrella patens. Plant J. 56, 855–866 (2008).
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom. Bioinform. 3, lqaa108 (2021).
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).
Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).
Tang, H. et al. Synteny and collinearity in plant genomes. Science 320, 486–488 (2008).
Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426 (1986).
Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics 13, 555–556 (1997).
Sensalari, C., Maere, S. & Lohaus, R. ksrates: positioning whole-genome duplications relative to speciation events in KS distributions. Bioinformatics 38, 530–532 (2021).
Proost, S. et al. i-ADHoRe 3.0-fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res. 40, e11 (2012).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
Laetsch, D. & Blaxter, M. KinFin: software for taxon-aware analysis of clustered protein sequences. G3 (Bethesda) 7, 3349–3357 (2017).
Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005).
Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Mirarab, S. et al. Astral: genome-scale coalescent-based species tree estimation. Bioinformatics 30, i541–i548 (2014).
Smith, S., Moore, M., Brown, J. W. & Yang, Y. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evol. Biol. 15, 150 (2015).
Smith, S. A., Brown, J. W. & Walker, J. F. So many genes, so little time: a practical approach to divergence-time estimation in the genomic era. PLoS ONE 13, e0197433 (2018).
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T. & Drummond, A. J. Beast 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).
Smith, S. A. & O’Meara, B. C. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28, 2689–2690 (2012).
Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).
Miklós, C. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26, 1910–1912 (2010).
Yi, Z. et al. Itak: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Mol. Plant 9, 1667–1670 (2016).
Kong, L. et al. Origins and evolution of cuticle biosynthetic machinery in land plants. Plant Physiol. 184, 1998–2010 (2020).
Whitewoods, C. D. et al. CLAVATA was a genetic novelty for the morphological innovation of 3D growth in land plants. Curr. Biol. 28, 2365–2376 (2018).
Radhakrishnan, G. V. et al. An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages. Nat. Plants 6, 280–289 (2020).
Wang, H., Kong, F. & Zhou, C. From genes to networks: the genetic control of leaf development. J. Integr. Plant Biol. 63, 1181–1196 (2021).
Xu, Z. et al. Genome analysis of the ancient tracheophyte Selaginella tamariscina reveals evolutionary features relevant to the acquisition of desiccation tolerance. Mol. Plant 11, 983–994 (2018).
Popper, Z. A. et al. Evolution and diversity of plant cell walls: from algae to flowering plants. Annu. Rev. Plant. Biol. 62, 567–590 (2011).
Fangel, J. U. et al. Cell wall evolution and diversity. Front. Plant Sci. 3, 152 (2012).
Cheng, S. et al. Genomes of subaerial Zygnematophyceae provide insights into land plant evolution. Cell 179, 1057–1067 (2019).
Wang, K. et al. The regulation of sporopollenin biosynthesis genes for rapid pollen wall formation. Plant Physiol. 178, 283–294 (2018).
Clayton, W. A. et al. UVR8-mediated induction of flavonoid biosynthesis for UVB tolerance is conserved between the liverwort Marchantia polymorpha and flowering plants. Plant J. 96, 503–517 (2018).
Jia, Q. et al. Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants. Proc. Natl Acad. Sci. USA 113, 12328–12333 (2016).
Mistry, J., Finn, R. D., Eddy, S. R., Bateman, A. & Punta, M. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 41, e121 (2013).
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641–1650 (2009).
Quang, M. B. et al. IQTREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Jin, M. et al. Two ABC transporters are differentially involved in the toxicity of two Bacillus thuringiensis Cry1 toxins to the invasive crop-pest Spodoptera frugiperda (J. E. Smith). Pest Manag. Sci. 77, 1492–1501 (2021).
Dong, S. Genome annotation files, orthogroup information, phylogenetic trees and alignments used for bryophyte genome project. figshare https://doi.org/10.6084/m9.figshare.23528667.v6 (2023).
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