Key: ⦿ corresponding author | * shared first
Under review
⦿[82] Kunz CF, Goldbecker ES, Darienko T, ⦿ de Vries J. Genome evolution: Zygnematophyceae on ice. Invited contribution at New Phytologist, under review
⦿[81] Zegers JMS, Irisarri I, de Vries S, ⦿ de Vries J. Evolving plant circuitries in streptophyte signalling cascades. Invited contribution at Journal of Cell Science, under review
[80] Schafran P, Hauser DA, Nelson JM, Xu X, Mueller LA, Kulshrestha S, Smalley I, de Vries S, Irisarri I, de Vries J, Davies K, Villarreal JCA, Li F-W. Pan-phylum genomes of hornworts revealed conserved autosomes but dynamic accessory and sex chromosomes.
⦿[79] Bierenbroodspot MJ, Darienko T, de Vries S, Pröschold T, Irisarri I, ⦿ de Vries J. Reply to Žárský and Eliáš: Robust Klebsormidiophyceae and an enigmatic Streptofilum.
[78] Ai G, Li T, Yang Z, de Vries J, Li G, Li Y, Li X, Lu X, Zhao Y, Shen D, Duo D. An ancient stress-regulatory suppressor of PP2C-As pre-dating PYL.
⦿[77] Rieseberg TP, Holzhausen A, Bierenbroodspot MJ, Zhang W, Abre u IN, ⦿ de Vries J. Conserved carotenoid pigmentation in reproductive organs of Charophyceae. Invited contribution at Phil Trans Roy Soc B, major revision requested
⦿[76] Fernie A, de Vries S, ⦿ de Vries J. Evolution of plant metabolism: the state-of-the-art. Invited contribution at Phil Trans Roy Soc B, minor revision
⦿[75] Dhabalia Ashok A, de Vries S, Irisarri I, ⦿ de Vries J. Evolutionary assembly of the plant terrestrialization toolkit from protein domains. Under review
⦿[74] Irisarri I, Lorente-Martínez H, Strassert JFH, Agorreta A, Zardoya R, San Mauro D, ⦿ de Vries J. Early diversification of membrane intrinsic proteins (MIP) in eukaryotes. minor revision requested at GBE
Available as preprint
⦿[73] Rieseberg TP, Dadras A, Darienko T, Post S, Herrfurth C, Fürst-Jansen JMR, Hohnhorst N, Petroll R, Rensing SA, Pröschold T, de Vries S, Irisarri I, Feussner I, ⦿ de Vries J. Time-resolved oxidative signal convergence across the algae–embryophyte divide. bioRxiv
[72] Karbstein K, Tomasello, Wagner ND, Barke BH, Pätzold C, Bradican JP, Dreieck M, Irisarri I, de Vries J, Hoerandl E. Efficient hybrid strategies for assembling the plastome, mitochondriome, and large nuclear genome of diploid Ranunculus cassubicifolius (Ranunculaceae). available on bioRxiv https://doi.org/10.1101/2023.08.08.552429
Published
2024
⦿[71] Goldbecker ES, Irisarri I, ⦿ de Vries J. The recurrent evolution of seaweed body plan complexity among photosynthetic eukaryotes. Molecular Plant, in press
⦿[70] Bierenbroodspot MJ, Pröschold T, Fürst-Jansen JMR, de Vries S, Irisarri I, Darienko T,. ⦿ de Vries J. Phylogeny and evolution of streptophyte algae. Invited contribution at Annals of Botany, imcae091, https://doi.org/10.1093/aob/mcae091
⦿[69] Kunz CF, de Vries S, ⦿ de Vries J. Plant terrestrialization: an environmental pull on the evolution of multi-sourced streptophyte phenolics. Invited contribution at Philosophical Transactions of the Royal Society B, in press
⦿[68] Feng X, Zheng J, Irisarri I, [45 co-authors] ⦿ de Vries J*, Yin Y*. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nature Genetics (2024). 56: 1018–1031. https://doi.org/10.1038/s41588-024-01737-3
[67] Keyl A, Herrfurth C, Pandey G, Kim R, Helwig L, Haslam T, de Vries S, de Vries J, Gutsche N, Zachgo S, Suh MC, Kunst J, Feussner I. Wax on, wax off: the divergent evolution of the alcohol-forming pathway of wax biosynthesis among land plants. New Phytologist early view, https://doi.org/10.1111/nph.19687
⦿[66] Dhabalia Ashok A, Freitag JN, Irisarri I, de Vries S, ⦿ de Vries J. Sequence similarity networks bear out hierarchical relationships of green cytochrome P450. Physiologia Plantarum 176: e14244. doi: 10.1111/ppl.14244. (2024)
[65] Madoukhi MSY, Rapp J, Irisarri I, Gunka K, Link H, Marienhagen J, de Vries J, Stuelke J, Commichau FM. Metabolic rewiring compensates for the loss of glutamate and aspartate biosynthesis in Bacillus subtilis. Microbial Biotechnology 17:e14429 (2024)
[64] Kunz H-H, Armbruster U, de Vries J, Davis GA. Chloroplast ion homeostasis – what do we know and where should we go? New Phytologist early view https://doi.org/10.1111/nph.19661
⦿[63] Bierenbroodspot MJ, Darienko T, de Vries S, Fürst-Jansen JMR, Buschmann H, Pröschold T, Irisarri I, ⦿ de Vries J. Phylogenomic insights into the first multicellular streptophyte. Current Biology 34:670-681.e7. doi: 10.1016/j.cub.2023.12.070
[62] Karbstein K, Kösters L, Hodač L, Hofmann M, Hörandl E, Tomasello S, Wagner N, Emerson BC, Albach DC, Scheu S, Bradler S, de Vries J, Irisarri I, Li H, Soltis P, Mäder P, Wäldchen J. Species Delimitation 4.0: Integrative Taxon-omics and Artificial Intelligence. Trends in Ecology and Evolution In press, online https://doi.org/10.1016/j.tree.2023.11.002
[61] Hembach L, Niemeyer PW, Schmitt K, Zegers JMS, Brandt D, Dabisch JJ, Valerius O, Braus GH, Schwarzländer M, de Vries J, Rensing SA, Ischebeck T. Proteome plasticity during Physcomitrium patens spore germination – from desiccation tolerance to heterotrophic growth and reconstitution of photoautotrophy. Plant Journal 117: 1466-1486
2023
⦿[60] Rieseberg TP, Dadras A, Bergschmidt LIN, Bierenbroodspot MJ, Fürst-Jansen JMR, Irisarri I, de Vries S, Darienko T, ⦿ de Vries J. Divergent responses to desiccation experiments in two ecophysiologically different Zygnematophyceae. Physiologia Plantarum 175:e14056. (2023)
[59] Pri-Tal O, Yufei S, Dadras A, Fürst-Jansen JMR, Zimran G, Michaeli D, Wijerathna-Yapa A, Shpilman M, Merilo E, Yarmolinsy D, Efroni I, de Vries J, Kollist H, Mosquna A. Constitutive activation of ABA receptors in Arabidopsis reveals unique regulatory circuitries. New Phytologist https://doi.org/10.1111/nph.19363
[58] de Vries S, Herrfurth C, Li F-W, Feussner I, de Vries J. An ancient route towards salicylic acid and its implications for the perpetual Trichormus–Azolla symbiosis. Plant, Cell & Environment 46:2884-2908. (2023)
⦿[57] Dadras A, Fürst-Jansen JMR, Darienko T, Krone D, Scholz P, Sun S, Herrfurth C, Rieseberg TP, Irisarri I, Steinkamp R, Hansen M, Buschmann H, Valerius O, Braus GH, Hoecker U, Feussner I, Mutwil M, Ischebeck T, de Vries S, Lorenz M, ⦿ de Vries J. Environmental gradients reveal stress hubs predating plant terrestrialization. Nature Plants 9:1419-1438. (2023)
⦿[56] Van de Poel B, ⦿ de Vries J. Evolution of ethylene as an abiotic stress hormone in streptophytes. Environmental and Experimental Botany 214: 105456. (2023)
[55] McCourt R, Lewis LA, Strother PK, Delwiche CF, Wickett NJ, de Vries J, Bowman J. Green land: multiple perspectives on green algal evolution and the earliest land plants. Invited article American Journal of Botany 110: e16175. (2023)
⦿[54] Dadras A, Rieseberg TP, Zegers JMS, Fürst-Jansen JMR, Irisarri I, ⦿ de Vries J, de Vries S. Accessible versatility underpins the deep evolution of plant specialized metabolism. Invited article Phytochemistry Reviews in press
[53] Mueller K-K, Pfeifer L, Schuldt L, Szövényi P, de Vries S, de Vries J, Johnson KL, Classen B. Fern cell walls and the evolution of arabinogalactan-proteins in streptophytes. Plant Journal 114: 875-894. | cover
[52] Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-Lopez MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel A-M, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J, The European Reference Genome Atlas Consortium. How genomics can help biodiversity conservation. Trends in Genetics online ahead of print https://doi.org/10.1016/j.tig.2023.01.005
⦿[51] Rieseberg TP, Dadras A, Fürst-Jansen JMR, Dhabalia Ashok A, Darienko T, de Vries S, Irisarri I, ⦿ de Vries J. Crossroads in the evolution of plant specialized metabolism. invited review Seminars in Cell and Developmental Biology, 134:37-58 (2023)
2022
[50] Niemeyer PW, Irisarri I, Scholz P, Schmitt K, Valerius O, Braus GH, Sharma S, Carlsson AS, de Vries J, Hofvander P, Ischebeck T. A seed-like proteome in oil rich tubers. Plant Journal 112: 518-534 (2022)
⦿[49] Hess S, Williams SK, Busch A, Irisarri I, Delwiche CF, de Vries S, Darienko T, Roger AJ, Archibald JM, Buschmann H, von Schwartzenberg K, ⦿ de Vries J. A phylogenomically informed five-order system for the closest relatives of land plants. Current Biology 32: 4473-4482 (2022)
⦿[48] Irisarri I, ⦿ de Vries J. Punctuated ancestral gene gains in streptophyte evolution. Molecular Plant 15:799-801 (2022)
⦿[47] de Vries S, ⦿ de Vries J. Evolutionary genomic insights into cyanobacterial symbioses in plants. invited review Quantitative Plant Biology 3:e16, 1–13 (2022)
[46] Pucker B, Irisarri I, de Vries J, Xu B. Plant genome sequence assembly 3.0: progress, challenges, and future directions. invited review Quantitative Plant Biology 3:e5 (2022)
[45] von Pappenheim F, Wensien M, Ye J, Uranga J, Irisarri I, de Vries J, Funk L-M, Mata R, Tittmann K. Widespread occurrence of covalent lysine–cysteine redox switches in proteins. Nature Chemical Biology (2022) 18: 368–375 (2022)
[44] Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-Lopez MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel A-M, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M, The European Reference Genome Atlas Consortium. The era of reference genomes in conservation genomics. Trends in Ecology and Evolution 37:197-202 (2022)
⦿[43] Fürst-Jansen JMR, de Vries S, Lorenz M, von Schwartzenberg K, Archibald JM, ⦿ de Vries J. Submergence of the filamentous Zygnematophyceae Mougeotia induces differential gene expression patterns associated with core metabolism and photosynthesis. Protoplasma doi: 10.1007/s00709-021-01730-1 (2022)
2021
⦿[42] Irisarri I, Darienko T, Pröschold T, Fürst-Jansen JMR, Jamy M, ⦿ de Vries J. Unexpected cryptic species among streptophyte algae most distant to land plants. Proceedings of the Royal Society B 288:20212168. (2021) | cover contribution
[41] Wickell D, Kuo L-Y, Yang H-P, Dhabalia Ashok A, Irisarri I, Dadras A, de Vries S, de Vries J, Huang Y-M, Li Z, Barker M, Hartwick N, Michael T, Li F-W. Underwater CAM photosynthesis elucidated by Isoetes genome. Nature Communications 12:6348. (2021)
[40] Völkner C, Holzer LJ, Day PM, Dhabalia Ashok A, de Vries J, Bölter B, Kunz H-H. Two plastid POLLUX ion channel-like proteins are required for stress-triggered stromal Ca2+ release. Plant Physiology 187:2110-2125. (2021)
⦿[39] de Vries S, Fürst-Jansen JMR, Irisarri I, Dhabalia Ashok A, Ischebeck T, Feussner K, Abreu IN, Petersen M, Feussner I, ⦿ de Vries J. The evolution of the phenylpropanoid pathway entailed pronounced radiation and divergence of enzyme families. Plant Journal 107:975-1002 (2021) | Research Highlight | Cover contribution
[38] Pyc M, Gidda S, Seay D, Esnay N, Kretzschmar F, Cai Y, Doner N, Greer M, Hull J, Coulon D, Bréhélin C, Yurchenko O, de Vries J, Valerius O, Braus G, Ischebeck T, Chapman K, Dyer J, Mullen R. LDIP cooperates with SEIPIN and LDAP to facilitate lipid droplet biogenesis in plants. Plant Cell 33:3076-3103 (2021)
[37] Resemann H, Herrfurth C, Feussner K, Hornung E, Ostendorf A, Gömann J, Mittag J, van Gessel N, de Vries J, Ludwig-Müller J, Markham J, Reski R, Feussner I. Convergence of sphingolipid desaturation across over 500 million years of plant evolution. Nature Plants 7: 219-232 (2021)
2020
[36] de Vries S, de Vries J, Archibald JM, Slamovits CH. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiology Ecology 96:fiaa184 (2020)
⦿[35] ⦿ de Vries J, Ischebeck T. Ties between stress and lipid droplets pre-date seeds. Trends in Plant Science 12: 1203-1214. (2020)
⦿[34] de Vries S, ⦿ de Vries J. A global evolutionary analysis of Carbohydrate-Esterase family 1 and 10 in oomycetes. Frontiers in Genetics 11:756 (2020)
⦿[33] ⦿ de Vries J*, de Vries S*, Curtis BA, Zhou H, Penny S, Feussner K, Pinto DM, Steinert M, Cohen A, von Schwartzenberg K, Archibald JM. Heat stress response in the closest algal relatives of land plants reveals conserved stress signalling circuits. Plant Journal 103:1025-1048 (2020) | Outstanding Original Research Article Award
⦿[32] de Vries S, ⦿ de Vries J. Plant genome evolution: meat lovers expanded gene families for carnivory and dropped the rest. Current Biology 30: R700-R702 (2020)
[31] Li F-W, Nishiyama T, Frangedakis E, Keller J, Li Z, Pozo N, Waller M, Barker M, Bennett T, Chen S, Cuming A, de Vries J, [21 co-authors] Szövényi P. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nature Plants 6:259–272 (2020).
⦿[30] Fürst-Jansen JMR, de Vries S, ⦿ de Vries J. Evo-physio: on stress responses and the earliest land plants. Journal of Experimental Botany 71:3254-3269 (2020) | High Impact Research from the Journal of Experimental Botany: Most cited
⦿[29] ⦿ de Vries J, Rensing SA. Gene gains paved the path to land. Nature Plants 6:7-8 (2020).
2019
[28] Sun Y, Harpazi B, Wijerathna-Yapa A, Merilo E, de Vries J, Michaeli D, Gal M, Cuming A, Kollist H, Mosquna A. A ligand-independent origin of abscisic acid perception. Proceedings of the National Academy of Sciences of the USA 116:24892-24899 (2019). | press coverage (multiple, including Phys.org and local newspapers)
[27] Delaux P-M, Hetherington AJ, Coudert Y, Delwiche C, Dolan L, Dunand C, Gould S, Kenrick P, Li F-W, Philippe H, Rensing SA, Rich M, Strullu-Derrien C, de Vries J. Reconstructing trait evolution in plant evo–devo studies. Current Biology 29: R1105–R1121 (2019).
[26] de Vries S, de Vries J, Rose LE. The elaboration of miRNA regulation and gene regulatory networks in plant-microbe interactions. Genes 10: 340. invited contribution (2019)
2018
[25] Nishiyama T, Sakayama H, de Vries J, [56 co-authors], Rensing SA. The Chara genome: secondary complexity and implications for plant terrestrialization. Cell 174: 448–464. (2018) | cover contribution | press coverage (multiple, including Phys.org) | F1000 recommendation
[24] de Vries S*, de Vries J*, von Dahlen JK, Gould SB, Archibald JM, Rose LE, Slamovits CH. On plant defense signaling networks and early land plant evolution. Communicative and Integrative Biology 11: e1486168. (2018)
[23] Li F-W, Brouwer P, Carretero-Paulet L, Cheng S, de Vries J, [35 co-authors], Wong G, Pryer K. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants 4: 460–472. (2018) | cover contribution | press coverage (multiple, including Discover Magazine, Phys.org, Spiegel, Science Daily) | F1000 recommendation
⦿[22] ⦿ de Vries J, Curtis BA, Gould SB, Archibald JM. Embryophyte stress signaling evolved in the algal progenitors of land plants. Proceedings of the National Academy of Sciences of the USA 115: E3471-E3480. (2018) | cover contribution | press coverage (The Chronicle Herald, Focus Online)
⦿[21] ⦿ de Vries J, Archibald JM. Plastid genomes. Current Biology 28: R336–R337. (2018)
[20] Ramachandran P, Wang G, Augstein F, de Vries J, Carlsbecker A. Continuous root xylem formation and vascular acclimation to water deficit involves endodermal ABA signalling via miR165. Development 145: dev159202. (2018)
[19] de Vries S*, de Vries J*, Teschke H, von Dahlen JK, Rose LE, Gould SB. Jasmonic and salicylic acid response in the fern Azolla filiculoides and its cyanobiont. Plant, Cell & Environment 41: 2530-2548. (2018)
⦿[18] ⦿ de Vries J, Archibald JM. Plant evolution: landmarks on the path to terrestrial life. New Phytologist 217: 1428–1434. (2018)
[17] de Vries J, Gould SB. The monoplastidic bottleneck in algae and plant evolution. Journal of Cell Science 131: jcs203414. (2018)
2017
[16] Rauch C, Christa G, de Vries J, Woehle C, Gould SB. Mitochondrial genome assemblies of Elysia timida and Elysia cornigera and the response of mitochondrion-associated metabolism during starvation. Genome Biology and Evolution 9: 1873–1879. (2017)
[15] Handrich M, de Vries J, Gould SB, Serôdio J, Christa G. Ulvophyceaen photophysiology and research opportunities. Perspectives in Phycology 4: 83-92. (2017) | cover contribution
⦿[14] ⦿ de Vries J*, de Vries S*, Slamovits CH, Rose LE, Archibald JM. How embryophytic is the biosynthesis of phenylpropanoids and their derivatives in streptophyte algae? Plant and Cell Physiology 58: 934-945. (2017) | Editor’s choice | Research highlight | cover contribution
[13] Junker C, de Vries J, Eickhorst C, Schulz B. Each isolate of Hymenoscyphus fraxineus is an individualist as shown by exoenzyme and growth rate profiles. Baltic Forestry 23: 25-40. (2017)
⦿[12] ⦿ de Vries J, Archibald JM, Gould SB. The carboxy terminus of YCF1 contains a motif conserved throughout >500 million years of streptophyte evolution. Genome Biology and Evolution 9: 473-479. (2017)
[11] de Vries J, Archibald JM. Endosymbiosis: did plastids evolve from a freshwater cyanobacterium. Current Biology 27: R103-R105. (2017)
[10] Christa G, Cruz S, Jahns P, de Vries J, Cartaxana P, Esteves AC, Serôdio J, Gould SB. Photoprotection in a monophyletic branch of chlorophyte algae is independent of energy-dependent quenching (qE). New Phytologist 214: 1132-1144. (2017)
2016
[9] de Vries J, Stanton A, Archibald JM, Gould SB. Streptophyte terrestrialization in light of plastid evolution. Trends in Plant Science 21: 467-476. (2016) | cover contribution
⦿[8] ⦿ de Vries J*, Fischer AM*, Roettger M, Rommel S, Schluepmann H, Bräutigam A, Carlsbecker A, Gould SB. Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots. New Phytologist 209: 705-720. (2016)
2015
[7] Rauch C, de Vries J, Rommel S, Rose LE, Woehle C, Christa G, Laetz EM, Wägele H, Tielens AGM, Nickelsen J, Schumann T, Jahns P, Gould SB. Why it is time to look beyond algal genes in photosynthetic slugs. Genome Biology and Evolution 7: 2602-2607. (2015)
[6] de Vries J, Sousa FL, Bölter B, Soll J, Gould SB: YCF1: a green TIC? Plant Cell 27: 1827–1833. (2015)
[5] de Vries J, Woehle C, Christa G, Wägele H, Tielens AGM, Jahns P, Gould SB: Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs. Proceedings of the Royal Society B 282: 20142519. (2015) | cover contribution, press coverage (Spektrum), Editor’s choice: Plastid thieves escape starvation. Science 347: 733
2014
[4] de Vries J, Rauch C, Christa G, Gould SB: A sea slug’s guide to plastid symbiosis. Acta Societatis Botanicorum Poloniae 83: 415-421. (2014) | cover contribution
[3] de Vries J, Christa G, Gould SB: Plastid survival in the cytosol of animal cells. Trends in Plant Science 19: 347-350. (2014) | cover contribution
[2] Christa G, de Vries J, Jahns P, Gould SB: Switching off photosynthesis: the dark side of sacoglossan slugs. Communicative and Integrative Biology 7: e28029. (2014)
2013
[1] de Vries J*, Habicht J*, Woehle C, Huang C, Christa G, Wägele H, Nickelsen J, Martin WF, Gould SB: Is ftsH the key to plastid longevity in sacoglossan slugs? Genome Biology and Evolution 5: 2540-2548. (2013) | F1000 recommendation
Peer-Reviewed Book Chapters
2018
[B2] ⦿ de Vries S, de Vries J: Azolla – a model system for symbiotic nitrogen fixation and evolutionary developmental biology. In: Current Advances in Fern Research, ed: Elena Mª Fernández González, Springer: New York (2018)
[B1] ⦿ de Vries J, Archibald JM: Plastid autonomy versus nuclear control over plastid function. In: Advances in Botanical Research Volume 85 –Plastid Genome Evolution, eds: Shu-Miaw Chaw and Robert Jansen, Elsevier, Academic Press: New York (2018)