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6. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution

Author

Feng, Xuehuan, Zheng, Jinfang, Irisarri, Iker, Yu, Huihui, Zheng, Bo, Ali, Zahin, de Vries, Sophie, Keller, Jean, Fürst-Jansen, Janine MR, Dadras, Armin, Zegers, Jaccoline MS, Rieseberg, Tim P, Dhabalia Ashok, Amra, Darienko, Tatyana, Bierenbroodspot, Maaike J, Gramzow, Lydia, Petroll, Romy, Haas, Fabian B, Fernandez-Pozo, Noe, Nousias, Orestis, Li, Tang, Fitzek, Elisabeth, Grayburn, W Scott, Rittmeier, Nina, Permann, Charlotte, Rümpler, Florian, Archibald, John M, Theißen, Günter, Mower, Jeffrey P, Lorenz, Maike, Buschmann, Henrik, von Schwartzenberg, Klaus, Boston, Lori, Hayes, Richard D, Daum, Chris, Barry, Kerrie, Grigoriev, Igor V, Wang, Xiyin, Li, Fay-Wei, Rensing, Stefan A, Ben Ari, Julius, Keren, Noa, Mosquna, Assaf, Holzinger, Andreas, Delaux, Pierre-Marc, Zhang, Chi, Huang, Jinling, Mutwil, Marek, de Vries, Jan, and Yin, Yanbin

Subjects
Plant Biology, Biological Sciences, Genetics, Life on Land, Signal Transduction, Embryophyta, Evolution, Molecular, Phylogeny, Gene Regulatory Networks, Genome, Genome, Plant, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.

Published
2024

11. de Vries

Author

de Vries, Jan

Published
2009

18. Environmental gradients reveal stress hubs pre-dating plant terrestrialization

Author

Dadras, Armin, Fürst-Jansen, Janine M. R., Darienko, Tatyana, Krone, Denis, Scholz, Patricia, Sun, Siqi, Herrfurth, Cornelia, Rieseberg, Tim P., Irisarri, Iker, Steinkamp, Rasmus, Hansen, Maike, Buschmann, Henrik, Valerius, Oliver, Braus, Gerhard H., Hoecker, Ute, Feussner, Ivo, Mutwil, Marek, Ischebeck, Till, de Vries, Sophie, Lorenz, Maike, and de Vries, Jan

Published
2023
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19. The Added Diagnostic Value of Transcatheter CT Hepatic Arteriography for Intraprocedural Detection of Previously Unknown Colorectal Liver Metastases During Percutaneous Ablation and Impact on the Definitive Treatment Plan

Author

van der Lei, Susan, Opperman, Jip, Dijkstra, Madelon, Kors, Nikita, Boon, Rianne, van den Bemd, Bente A. T., Timmer, Florentine E. F., Nota, Irene M. G. C., van den Bergh, Janneke E., de Vries, Jan J. J., Scheffer, Hester J., Geboers, Bart, Neuss, Timothy, Schouten, Evelien, Lissenberg-Witte, Birgit I., Puijk, Robbert S., and Meijerink, Martijn R.

Published
2023
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20. Unresectable Intermediate-Size (3–5 cm) Colorectal Liver Metastases: Stereotactic Ablative Body Radiotherapy Versus Microwave Ablation (COLLISION-XL): Protocol of a Phase II/III Multicentre Randomized Controlled Trial

Author

van der Lei, Susan, Dijkstra, Madelon, Nieuwenhuizen, Sanne, Schulz, Hannah H., Vos, Danielle J. W., Versteeg, Kathelijn S., Buffart, Tineke E., Swijnenburg, Rutger-Jan, de Vries, Jan J. J., Bruynzeel, Anna M. E., van den Tol, M. Petrousjka, Scheffer, Hester J., Puijk, Robbert S., Haasbeek, Cornelis J. A., and Meijerink, Martijn R.

Published
2023
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21. MRI-guided stereotactic ablative body radiotherapy versus CT-guided percutaneous irreversible electroporation for locally advanced pancreatic cancer (CROSSFIRE): a single-centre, open-label, randomised phase 2 trial

Author

Timmer, Florentine E F, Geboers, Bart, Ruarus, Alette H, Vroomen, Laurien G P H, Schouten, Evelien A C, van der Lei, Susan, Vos, Danielle J W, Dijkstra, Madelon, Schulz, Hannah H, Bakker, Joyce, van den Bemd, Bente A T, van den Tol, Petrousjka M, Puijk, Robbert S, Lissenberg-Witte, Birgit I, de Gruijl, Tanja D, de Vries, Jan J J, Lagerwaard, Frank J, Scheffer, Hester J, Bruynzeel, Anna M E, and Meijerink, Martijn R

Published
2024
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25. Tissue Resistance Decrease during Irreversible Electroporation of Pancreatic Cancer as a Biomarker for the Adaptive Immune Response and Survival

Author

Timmer, Florentine E.F., Geboers, Bart, Scheffer, Hester J., Bakker, Joyce, Ruarus, Alette H., Dijkstra, Madelon, van der Lei, Susan, Boon, Rianne, Nieuwenhuizen, Sanne, van den Bemd, Bente A.T., Schouten, Evelien A.C., van den Tol, Petrousjka M., Puijk, Robbert S., de Vries, Jan J.J., de Gruijl, Tanja D., and Meijerink, Martijn R.

Published
2023
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27. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Author

Li, Fay-Wei, Nishiyama, Tomoaki, Waller, Manuel, Frangedakis, Eftychios, Keller, Jean, Li, Zheng, Fernandez-Pozo, Noe, Barker, Michael S, Bennett, Tom, Blázquez, Miguel A, Cheng, Shifeng, Cuming, Andrew C, de Vries, Jan, de Vries, Sophie, Delaux, Pierre-Marc, Diop, Issa S, Harrison, C Jill, Hauser, Duncan, Hernández-García, Jorge, Kirbis, Alexander, Meeks, John C, Monte, Isabel, Mutte, Sumanth K, Neubauer, Anna, Quandt, Dietmar, Robison, Tanner, Shimamura, Masaki, Rensing, Stefan A, Villarreal, Juan Carlos, Weijers, Dolf, Wicke, Susann, Wong, Gane K-S, Sakakibara, Keiko, and Szövényi, Péter

Subjects
Plant Biology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Anthocerotophyta, Biological Evolution, Embryophyta, Genome, Plant, Life History Traits, Crop and Pasture Production, Ecology, Plant biology
Abstract

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

Published
2020

28. Training Programmes for Practitioners in Sexual Health Promotion: An Integrative Literature Review of Evaluations

Author

Begley, Thelma, Daly, Louise, Downes, Carmel, De Vries, Jan, Sharek, Danika, and Higgins, Agnes

Abstract

This paper reports on findings from an integrative literature review of evaluation studies undertaken into sexual health promotion preparation programmes aimed at professionals with a sexual health promotion remit. Using a pre-defined search strategy, inclusion criteria and PRISMA guidelines, databases were systematically searched. Studies were screened and those included were quality assessed. Twenty-seven relevant studies were identified. Thematic analysis showed programmes were diverse in terms of how they had been developed, the content included, approaches to evaluation and outcomes identified. Evaluations showed participation in a training programme encouraged participants to feel more comfortable and confident to discuss sexual health within their role and more likely to introduce sexual health into client discussions. The types of programmes and evaluation approaches were diverse making direct comparison between them challenging. There should be agreed core outcome impact measures for sexual health education programmes in the areas of knowledge, comfort, skills and changes to practice, to allow for more direct comparison in future evaluation studies.

Published
2022
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29. How genomics can help biodiversity conservation

Author

Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim do Rosario, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe C., Chueca, Luis J., Čiampor, Fedor, Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Agius, Dolores R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Theissinger, Kathrin, Fernandes, Carlos, Formenti, Giulio, Bista, Iliana, Berg, Paul R., Bleidorn, Christoph, Bombarely, Aureliano, Crottini, Angelica, Gallo, Guido R., Godoy, José A., Jentoft, Sissel, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per J., Pampoulie, Christophe, Ruiz-López, María J., Secomandi, Simona, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Jarvis, Erich D., Bálint, Miklós, Ciofi, Claudio, Waterhouse, Robert M., Mazzoni, Camila J., and Höglund, Jacob

Published
2023
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34. Improved Outcomes of Thermal Ablation for Colorectal Liver Metastases: A 10-Year Analysis from the Prospective Amsterdam CORE Registry (AmCORE)

Author

Puijk, Robbert S., Dijkstra, Madelon, van den Bemd, Bente A. T., Ruarus, Alette H., Nieuwenhuizen, Sanne, Geboers, Bart, Timmer, Florentine E. F., Schouten, Evelien A. C., de Vries, Jan J. J., van der Meijs, Bram B., Nielsen, Karin, Swijnenburg, Rutger-Jan, van den Tol, M. Petrousjka, Versteeg, Kathelijn S., Lissenberg-Witte, Birgit I., Scheffer, Hester J., and Meijerink, Martijn R.

Published
2022
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36. Microwave Ablation, Radiofrequency Ablation, Irreversible Electroporation, and Stereotactic Ablative Body Radiotherapy for Intermediate Size (3–5 cm) Unresectable Colorectal Liver Metastases: a Systematic Review and Meta-analysis

Author

Nieuwenhuizen, Sanne, Dijkstra, Madelon, Puijk, Robbert S., Geboers, Bart, Ruarus, Alette H., Schouten, Evelien A., Nielsen, Karin, de Vries, Jan J. J., Bruynzeel, Anna M. E., Scheffer, Hester J., van den Tol, M. Petrousjka, Haasbeek, Cornelis J. A., and Meijerink, Martijn R.

Published
2022
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37. Species delimitation 4.0: integrative taxonomy meets artificial intelligence

Author

Federal Ministry of Education and Research (Germany), Ministry of Agriculture and Food (Germany), Federal Ministry for the Environment, Nature Conservation, Nuclear Safety, and Consumer Protection (Germany), German Research Foundation, European Commission, National Natural Science Foundation of China, Karbstein, Kevin [0000-0003-1424-6557], Kösters, Lara [0000-0002-7913-2377], Hodač, Ladislav [0000-0002-6885-1317], Hofmann, Martin [0000-0002-4440-3317], Hörandl, Elvira [0000-0002-7600-1128], Tomasello, Salvatore [0000-0001-5201-1156], Wagner, Natascha D. [0000-0001-6623-7623], Emerson, Brent C. [0000-0003-4067-9858], Albach , Dirk C. [0000-0001-9056-7382], Scheu, Stefan [0000-0003-4350-9520], Bradler, Sven [0000-0001-9307-1032], de Vries, Jan [0000-0003-3507-5195], Irisarri, Iker [0000-0002-3628-1137], Li, He [0000-0002-4591-8056], Pamela Soltis [0000-0001-9310-8659], Mäder, Patrick [0000-0001-6871-2707], Wäldchen, Jana [0000-0002-2631-1531], Karbstein, Kevin, Kösters, Lara, Hodač, Ladislav, Hofmann, Martin, Hörandl, Elvira, Tomasello, Salvatore, Wagner, Natascha D., Emerson, Brent C., Albach , Dirk C., Scheu, Stefan, Bradler, Sven, de Vries, Jan, Irisarri, Iker, Li, He, Pamela Soltis, Mäder, Patrick, Wäldchen, Jana, Federal Ministry of Education and Research (Germany), Ministry of Agriculture and Food (Germany), Federal Ministry for the Environment, Nature Conservation, Nuclear Safety, and Consumer Protection (Germany), German Research Foundation, European Commission, National Natural Science Foundation of China, Karbstein, Kevin [0000-0003-1424-6557], Kösters, Lara [0000-0002-7913-2377], Hodač, Ladislav [0000-0002-6885-1317], Hofmann, Martin [0000-0002-4440-3317], Hörandl, Elvira [0000-0002-7600-1128], Tomasello, Salvatore [0000-0001-5201-1156], Wagner, Natascha D. [0000-0001-6623-7623], Emerson, Brent C. [0000-0003-4067-9858], Albach , Dirk C. [0000-0001-9056-7382], Scheu, Stefan [0000-0003-4350-9520], Bradler, Sven [0000-0001-9307-1032], de Vries, Jan [0000-0003-3507-5195], Irisarri, Iker [0000-0002-3628-1137], Li, He [0000-0002-4591-8056], Pamela Soltis [0000-0001-9310-8659], Mäder, Patrick [0000-0001-6871-2707], Wäldchen, Jana [0000-0002-2631-1531], Karbstein, Kevin, Kösters, Lara, Hodač, Ladislav, Hofmann, Martin, Hörandl, Elvira, Tomasello, Salvatore, Wagner, Natascha D., Emerson, Brent C., Albach , Dirk C., Scheu, Stefan, Bradler, Sven, de Vries, Jan, Irisarri, Iker, Li, He, Pamela Soltis, Mäder, Patrick, and Wäldchen, Jana

Abstract

Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.

Published
2024

39. Current and future perspectives for enhancing our understanding of the evolution of plant metabolism.

Author

de Vries, Jan, de Vries, Sophie, and Fernie, Alisdair R.

Subjects
*PLANT metabolism, *PLANT evolution, *METABOLISM, *SPECIES
Abstract

The special issue 'The evolution of plant metabolism' has brought together original research, reviews and opinions that cover various aspects from the full breath of plant metabolism including its interaction with the environment including other species. Here, we briefly summarize these efforts and attempts to extract a consensus opinion of the best manner in which to tackle this subject both now and in the future. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Conserved carotenoid pigmentation in reproductive organs of Charophyceae.

Author

Rieseberg, Tim P., Holzhausen, Anja, Bierenbroodspot, Maaike J., Zhang, Wanchen, Abreu, Ilka N., and de Vries, Jan

Subjects
HIGH performance liquid chromatography, CHAROPHYTA, PLANT evolution, PLANT metabolism, PLANT proteins
Abstract

Sexual reproduction in Charophyceae abounds in complex traits. Their gametangia develop as intricate structures, with oogonia spirally surrounded by envelope cells and richly pigmented antheridia. The red—probably protectant—pigmentation of antheridia is conserved across Charophyceae. Chara tomentosa is, however, unique in exhibiting this pigmentation and also in vegetative tissue. Here, we investigated the two sympatric species, C. tomentosa and Chara baltica, and compared their molecular chassis for pigmentation. Using reversed phase C30 high performance liquid chromatography (RP-C30-HPLC), we uncover that the major pigments are β-carotene, δ-carotene and γ-carotene; using headspace solid-phase microextraction coupled to gas chromatography equipped with a mass spectrometer (HS-SPME-GC-MS), we pinpoint that the unusually large carotenoid pool in C. tomentosa gives rise to diverse volatile apocarotenoids, including abundant 6-methyl-5-hepten-2-one. Based on transcriptome analyses, we uncover signatures of the unique biology of Charophycaee and genes for pigment production, including monocyclized carotenoids. The rich carotenoid pool probably serves as a substrate for diverse carotenoid-derived metabolites, signified not only by (i) the volatile apocarotenoids we detected but (ii) the high expression of a gene coding for a cytochrome P450 enzyme related to land plant proteins involved in the biosynthesis of carotenoid-derived hormones. Overall, our data shed light on a key protection strategy of sexual reproduction in the widespread group of macroalgae. The genetic underpinnings of this are shared across hundreds of millions of years of plant and algal evolution. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Published
2024
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41. Plant terrestrialization: an environmental pull on the evolution of multi-sourced streptophyte phenolics.

Author

Kunz, Cäcilia F., de Vries, Sophie, and de Vries, Jan

Subjects
PHENOLS, PLANT metabolism, PLANT evolution, PHENYLPROPANOIDS, PLANT hormones
Abstract

Phenolic compounds of land plants are varied: they are chemodiverse, are sourced from different biosynthetic routes and fulfil a broad spectrum of functions that range from signalling phytohormones, to protective shields against stressors, to structural compounds. Their action defines the biology of land plants as we know it. Often, their roles are tied to environmental responses that, however, impacted already the algal progenitors of land plants, streptophyte algae. Indeed, many streptophyte algae successfully dwell in terrestrial habitats and have homologues for enzymatic routes for the production of important phenolic compounds, such as the phenylpropanoid pathway. Here, we synthesize what is known about the production of specialized phenolic compounds across hundreds of millions of years of streptophyte evolution. We propose an evolutionary scenario in which selective pressures borne out of environmental cues shaped the chemodiversity of phenolics in streptophytes. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Published
2024
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42. Evolution of plant metabolism: the state-of-the-art.

Author

Fernie, Alisdair R., de Vries, Sophie, and de Vries, Jan

Subjects
SECONDARY metabolism, HORIZONTAL gene transfer, METABOLISM, PLANT metabolism, PLANT evolution
Abstract

Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Published
2024
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43. The era of reference genomes in conservation genomics

Author

Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlos, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Čiampor, Fedor, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Hoglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per, Pampoulie, Christophe, Ruiz-López, María José, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Goujie, Mazzoni, Camila J., Jarvis, Erich, Bálint, Miklós, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Berg, Paul R., Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe, Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Waterhouse, Robert M., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Höglund, Jacob, Palsbøll, Per J., Ruiz-López, María J., Zhang, Guojie, and Jarvis, Erich D.

Published
2022
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45. Fern genomes elucidate land plant evolution and cyanobacterial symbioses.

Author

Li, Fay-Wei, Brouwer, Paul, Carretero-Paulet, Lorenzo, Cheng, Shifeng, de Vries, Jan, Delaux, Pierre-Marc, Eily, Ariana, Koppers, Nils, Kuo, Li-Yaung, Li, Zheng, Simenc, Mathew, Small, Ian, Wafula, Eric, Angarita, Stephany, Barker, Michael S, Bräutigam, Andrea, dePamphilis, Claude, Gould, Sven, Hosmani, Prashant S, Huang, Yao-Moan, Huettel, Bruno, Kato, Yoichiro, Liu, Xin, Maere, Steven, McDowell, Rose, Mueller, Lukas A, Nierop, Klaas GJ, Rensing, Stefan A, Robison, Tanner, Rothfels, Carl J, Sigel, Erin M, Song, Yue, Timilsena, Prakash R, Van de Peer, Yves, Wang, Hongli, Wilhelmsson, Per KI, Wolf, Paul G, Xu, Xun, Der, Joshua P, Schluepmann, Henriette, Wong, Gane K-S, and Pryer, Kathleen M

Subjects
Cyanobacteria, Ferns, Phylogeny, Symbiosis, Gene Duplication, Genes, Plant, Genome, Plant, Biological Evolution, Genes, Plant, Genome
Abstract

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

Published
2018

48. Phylogeny and evolution of streptophyte algae

Author

Bierenbroodspot, Maaike, primary, Pröschold, Thomas, additional, Fürst-Jansen, Janine M R, additional, de Vries, Sophie, additional, Irisarri, Iker, additional, Darienko, Tatyana, additional, and de Vries, Jan, additional

Published
2024
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