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1. 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

4. An optimized transformation protocol for Anthoceros agrestis and three more hornwort species

Author

Waller, Manuel, Frangedakis, Eftychios, Marron, Alan O, Sauret-Güeto, Susanna, Rever, Jenna, Sabbagh, Cyrus Raja Rubenstein, Hibberd, Julian M, Haseloff, Jim, Renzaglia, Karen S, Szövényi, Péter, Waller, Manuel [0000-0002-6060-0740], Frangedakis, Eftychios [0000-0002-3483-8464], Marron, Alan O [0000-0002-2606-5641], Sauret-Güeto, Susanna [0000-0003-3792-8278], Sabbagh, Cyrus Raja Rubenstein [0000-0003-3866-8332], Hibberd, Julian M [0000-0003-0662-7958], Haseloff, Jim [0000-0003-4793-8058], Szövényi, Péter [0000-0002-0324-4639], and Apollo - University of Cambridge Repository

Subjects
subcellular targeting, hornworts, Agrobacterium-mediated transformation, Seeds, Genetics, Embryophyta, Anthocerotophyta, land plant evolution, Bryophyta, Cell Biology, Plant Science, constitutive promoter, Phylogeny
Abstract

Funder: Georges and Antoine Claraz Foundation grant, Funder: University Research Priority Program “Evolution in Action” of the University of Zurich, Land plants comprise two large monophyletic lineages, the vascular plants and the bryophytes, which diverged from their most recent common ancestor approximately 480 million years ago. Of the three lineages of bryophytes, only the mosses and the liverworts are systematically investigated, while the hornworts are understudied. Despite their importance for understanding fundamental questions of land plant evolution, they only recently became amenable to experimental investigation, with Anthoceros agrestis being developed as a hornwort model system. Availability of a high-quality genome assembly and a recently developed genetic transformation technique makes A. agrestis an attractive model species for hornworts. Here we describe an updated and optimized transformation protocol for A. agrestis, which can be successfully used to genetically modify one more strain of A. agrestis and three more hornwort species, Anthoceros punctatus, Leiosporoceros dussii, and Phaeoceros carolinianus. The new transformation method is less laborious, faster, and results in the generation of greatly increased numbers of transformants compared with the previous method. We have also developed a new selection marker for transformation. Finally, we report the development of a set of different cellular localization signal peptides for hornworts providing new tools to better understand the hornwort cell biology.

Published
2023
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8. An optimised transformation protocol for Anthoceros agrestis and three more hornwort species

Author

Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Marron, Alan O, Sauret-Gueto, Susanna, Rever, Jenna, Sabbagh, Cyrus Raja Rubenstein, Hibberd, Julian M; https://orcid.org/0000-0003-0662-7958, Haseloff, Jim; https://orcid.org/0000-0003-4793-8058, Renzaglia, Karen S, Szövényi, Péter; https://orcid.org/0000-0002-0324-4639, Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Marron, Alan O, Sauret-Gueto, Susanna, Rever, Jenna, Sabbagh, Cyrus Raja Rubenstein, Hibberd, Julian M; https://orcid.org/0000-0003-0662-7958, Haseloff, Jim; https://orcid.org/0000-0003-4793-8058, Renzaglia, Karen S, and Szövényi, Péter; https://orcid.org/0000-0002-0324-4639

Abstract

Land plants comprise two large monophyletic lineages, the vascular plants and the bryophytes, which diverged from their most recent common ancestor approximately 480 million years ago. Of the three lineages of bryophytes, only the mosses and the liverworts are systematically investigated, while the hornworts are understudied. Despite their importance for understanding fundamental questions of land plant evolution, they only recently became amenable to experimental investigation, with Anthoceros agrestis being developed as a hornwort model system. Availability of a high-quality genome assembly and a recently developed genetic transformation technique makes A. agrestis an attractive model species for hornworts. Here we describe an updated and optimised transformation protocol for A. agrestis which can be successfully used to genetically modify one more strain of A. agrestis and three more hornwort species, Anthoceros punctatus, Leiosporoceros dussi and Phaeoceros carolinianus. The new transformation method is less laborious, faster and results in the generation of greatly increased numbers of transformants compared to the previous method. We have also developed a new selection marker for transformation. Finally, we report the development of a set of different cellular localisation signal peptides for hornworts providing new tools to better understand hornwort cell biology.

Published
2023

9. What can hornworts teach us?

Author

Frangedakis, Eftychios, Marron, Alan O, Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Neubauer, Anna; https://orcid.org/0000-0002-5102-2491, Tse, Sze Wai, Yue, Yuling, Ruaud, Stéphanie; https://orcid.org/0000-0001-7698-0605, Waser, Lucas, Sakakibara, Keiko, Szövényi, Péter; https://orcid.org/0000-0002-0324-4639, Frangedakis, Eftychios, Marron, Alan O, Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Neubauer, Anna; https://orcid.org/0000-0002-5102-2491, Tse, Sze Wai, Yue, Yuling, Ruaud, Stéphanie; https://orcid.org/0000-0001-7698-0605, Waser, Lucas, Sakakibara, Keiko, and Szövényi, Péter; https://orcid.org/0000-0002-0324-4639

Abstract

The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

Published
2023

10. What can hornworts teach us?

Author

Frangedakis, Eftychios, primary, Marron, Alan O., additional, Waller, Manuel, additional, Neubauer, Anna, additional, Tse, Sze Wai, additional, Yue, Yuling, additional, Ruaud, Stephanie, additional, Waser, Lucas, additional, Sakakibara, Keiko, additional, and Szövényi, Péter, additional

Published
2023
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11. Step-by-step protocol for the isolation and transient transformation of hornwort protoplasts

Author

Neubauer, Anna, Ruaud, Stéphanie, Waller, Manuel, Frangedakis, Eftychios, Li, Fay-Wei, Nötzold, Svenja I, Wicke, Susann, Bailly, Aurélien, Szövényi, Péter, Neubauer, Anna [0000-0002-5102-2491], Ruaud, Stéphanie [0000-0001-7698-0605], Waller, Manuel [0000-0002-6060-0740], Frangedakis, Eftychios [0000-0002-3483-8464], Li, Fay-Wei [0000-0002-0076-0152], Wicke, Susann [0000-0001-5785-9500], Bailly, Aurélien [0000-0001-5546-1945], Szövényi, Péter [0000-0002-0324-4639], and Apollo - University of Cambridge Repository

Subjects
hornworts, protoplasts, PROTOCOL NOTE, fungi, food and beverages, transient transformation, Anthoceros, model organism
Abstract

Premise: A detailed protocol for the protoplast transformation of hornwort tissue is not yet available, limiting molecular biological investigations of these plants and comparative analyses with other bryophytes, which display a gametophyte-dominant life cycle and are critical to understanding the evolution of key land plant traits. Methods and Results: We describe a detailed protocol to isolate and transiently transform protoplasts of the model hornwort Anthoceros agrestis. The digestion of liquid cultures with Driselase yields a high number of viable protoplasts suitable for polyethylene glycol (PEG)-mediated transformation. We also report early signs of protoplast regeneration, such as chloroplast division and cell wall reconstitution. Conclusions: This protocol represents a straightforward method for isolating and transforming A. agrestis protoplasts that is less laborious than previously described approaches. In combination with the recently developed stable genome transformation technique, this work further expands the prospects of functional studies in this model hornwort.

Published
2022

13. Step‐by‐step protocol for the isolation and transient transformation of hornwort protoplasts

Author

Neubauer, Anne; https://orcid.org/0000-0002-5102-2491, Ruaud, Stéphanie; https://orcid.org/0000-0001-7698-0605, Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Li, Fay‐Wei; https://orcid.org/0000-0002-0076-0152, Nötzold, Svenja I, Wicke, Susann; https://orcid.org/0000-0001-5785-9500, Bailly, Aurélien; https://orcid.org/0000-0001-5546-1945, Szövényi, Péter; https://orcid.org/0000-0002-0324-4639, Neubauer, Anne; https://orcid.org/0000-0002-5102-2491, Ruaud, Stéphanie; https://orcid.org/0000-0001-7698-0605, Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Li, Fay‐Wei; https://orcid.org/0000-0002-0076-0152, Nötzold, Svenja I, Wicke, Susann; https://orcid.org/0000-0001-5785-9500, Bailly, Aurélien; https://orcid.org/0000-0001-5546-1945, and Szövényi, Péter; https://orcid.org/0000-0002-0324-4639

Abstract

Premise: A detailed protocol for the protoplast transformation of hornwort tissue is not yet available, limiting molecular biological investigations of these plants and comparative analyses with other bryophytes, which display a gametophyte‐dominant life cycle and are critical to understanding the evolution of key land plant traits. Methods and Results: We describe a detailed protocol to isolate and transiently transform protoplasts of the model hornwort Anthoceros agrestis. The digestion of liquid cultures with Driselase yields a high number of viable protoplasts suitable for polyethylene glycol (PEG)‐mediated transformation. We also report early signs of protoplast regeneration, such as chloroplast division and cell wall reconstitution. Conclusions: This protocol represents a straightforward method for isolating and transforming A. agrestis protoplasts that is less laborious than previously described approaches. In combination with the recently developed stable genome transformation technique, this work further expands the prospects of functional studies in this model hornwort.

Published
2022

14. Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

Author

Kirbis, Alexander, primary, Rahmatpour, Nasim, additional, Dong, Shanshan, additional, Yu, Jin, additional, van Gessel, Nico, additional, Waller, Manuel, additional, Reski, Ralf, additional, Lang, Daniel, additional, Rensing, Stefan A., additional, Temsch, Eva M., additional, Wegrzyn, Jill L., additional, Goffinet, Bernard, additional, Liu, Yang, additional, and Szövényi, Péter, additional

Published
2022
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15. Step‐by‐step protocol for the isolation and transient transformation of hornwort protoplasts

Author

Neubauer, Anne, Ruaud, Stéphanie, Waller, Manuel, Frangedakis, Eftychios, Li, Fay‐Wei, Nötzold, Svenja I, Wicke, Susann, Bailly, Aurélien, Szövényi, Péter, and University of Zurich

Subjects
UFSP13-7 Evolution in Action: From Genomes to Ecosystems, 10121 Department of Systematic and Evolutionary Botany, 10126 Department of Plant and Microbial Biology, Ecology, Behavior and Systematics, Evolution, Plant Science, 580 Plants (Botany), 10211 Zurich-Basel Plant Science Center
Published
2022
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20. Immunogenicity and Safety of the BNT162b2 mRNA COVID-19 Vaccine Among Actively Treated Cancer Patients

Author

Ligumsky, Hagai, primary, Safadi, Esraa, additional, Etan, Tal, additional, Vaknin, Noam, additional, Waller, Manuel, additional, Croll, Assaf, additional, Nikolaevski-Berlin, Alla, additional, Greenberg, Inbal, additional, Halperin, Tami, additional, Wasserman, Asaf, additional, Galazan, Lior, additional, Arber, Nadir, additional, and Wolf, Ido, additional

Published
2021
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21. A simple Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis

Author

Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Waller, Manuel, Nishiyama, Tomoaki, Tsukaya, Hirokazu; https://orcid.org/0000-0002-4430-4538, Xu, Xia, Yue, Yuling, Tjahjadi, Michelle, Gunadi, Andika; https://orcid.org/0000-0002-0097-6906, Van Eck, Joyce; https://orcid.org/0000-0002-8005-365X, Li, Fay-Wei; https://orcid.org/0000-0002-0076-0152, Szövényi, Péter; https://orcid.org/0000-0002-0324-4639, Sakakibara, Keiko, Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Waller, Manuel, Nishiyama, Tomoaki, Tsukaya, Hirokazu; https://orcid.org/0000-0002-4430-4538, Xu, Xia, Yue, Yuling, Tjahjadi, Michelle, Gunadi, Andika; https://orcid.org/0000-0002-0097-6906, Van Eck, Joyce; https://orcid.org/0000-0002-8005-365X, Li, Fay-Wei; https://orcid.org/0000-0002-0076-0152, Szövényi, Péter; https://orcid.org/0000-0002-0324-4639, and Sakakibara, Keiko

Published
2021

22. An Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis

Author

Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Nishiyama, Tomoaki; https://orcid.org/0000-0003-1279-7806, Tsukaya, Hirokazu; https://orcid.org/0000-0002-4430-4538, Xu, Xia, Yue, Yuling, Tjahjadi, Michelle, Gunadi, Andika; https://orcid.org/0000-0002-0097-6906, Van Eck, Joyce; https://orcid.org/0000-0002-8005-365X, Li, Fay‐Wei; https://orcid.org/0000-0002-0076-0152, Szövényi, Péter; https://orcid.org/0000-0002-0324-4639, Sakakibara, Keiko; https://orcid.org/0000-0003-4420-9351, Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Nishiyama, Tomoaki; https://orcid.org/0000-0003-1279-7806, Tsukaya, Hirokazu; https://orcid.org/0000-0002-4430-4538, Xu, Xia, Yue, Yuling, Tjahjadi, Michelle, Gunadi, Andika; https://orcid.org/0000-0002-0097-6906, Van Eck, Joyce; https://orcid.org/0000-0002-8005-365X, Li, Fay‐Wei; https://orcid.org/0000-0002-0076-0152, Szövényi, Péter; https://orcid.org/0000-0002-0324-4639, and Sakakibara, Keiko; https://orcid.org/0000-0003-4420-9351

Published
2021

23. The hornworts: morphology, evolution and development

Author

Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Shimamura, Masaki; https://orcid.org/0000-0002-5665-5116, Villarreal, Juan Carlos; https://orcid.org/0000-0002-0770-1446, Li, Fay‐Wei; https://orcid.org/0000-0002-0076-0152, Tomaselli, Marta; https://orcid.org/0000-0003-3470-2820, Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Sakakibara, Keiko; https://orcid.org/0000-0003-4420-9351, Renzaglia, Karen S; https://orcid.org/0000-0002-1406-2646, Szövényi, Péter; https://orcid.org/0000-0002-0324-4639, Frangedakis, Eftychios; https://orcid.org/0000-0002-3483-8464, Shimamura, Masaki; https://orcid.org/0000-0002-5665-5116, Villarreal, Juan Carlos; https://orcid.org/0000-0002-0770-1446, Li, Fay‐Wei; https://orcid.org/0000-0002-0076-0152, Tomaselli, Marta; https://orcid.org/0000-0003-3470-2820, Waller, Manuel; https://orcid.org/0000-0002-6060-0740, Sakakibara, Keiko; https://orcid.org/0000-0003-4420-9351, Renzaglia, Karen S; https://orcid.org/0000-0002-1406-2646, and Szövényi, Péter; https://orcid.org/0000-0002-0324-4639

Abstract

Extant land plants consist of two deeply divergent groups, tracheophytes and bryophytes, which shared a common ancestor some 500 million years ago. While information about vascular plants and the two of the three lineages of bryophytes, the mosses and liverworts, is steadily accumulating, the biology of hornworts remains poorly explored. Yet, as the sister group to liverworts and mosses, hornworts are critical in understanding the evolution of key land plant traits. Until recently, there was no hornwort model species amenable to systematic experimental investigation, which hampered detailed insight into the molecular biology and genetics of this unique group of land plants. The emerging hornwort model species, Anthoceros agrestis, is instrumental in our efforts to better understand not only hornwort biology but also fundamental questions of land plant evolution. To this end, here we provide an overview of hornwort biology and current research on the model plant A. agrestis to highlight its potential in answering key questions of land plant biology and evolution.

Published
2021

24. A simple Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis

Author

Frangedakis, Eftychios, primary, Waller, Manuel, additional, Nishiyama, Tomoaki, additional, Tsukaya, Hirokazu, additional, Xu, Xia, additional, Yue, Yuling, additional, Tjahjadi, Michelle, additional, Gunadi, Andika, additional, Van Eck, Joyce, additional, Li, Fay-Wei, additional, Szövényi, Péter, additional, and Sakakibara, Keiko, additional

Published
2021
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25. The hornworts: morphology, evolution and development

Author

Frangedakis, Eftychios, primary, Shimamura, Masaki, additional, Villarreal, Juan Carlos, additional, Li, Fay‐Wei, additional, Tomaselli, Marta, additional, Waller, Manuel, additional, Sakakibara, Keiko, additional, Renzaglia, Karen S., additional, and Szövényi, Péter, additional

Published
2020
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27. Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica

Author

Kirbis, Alexander, Waller, Manuel, Ricca, Mariana, Bont, Zoe, Neubauer, Anna, Goffinet, Bernard, Szövényi, Péter, University of Zurich, and Szövényi, Péter

Subjects
Funariaceae, 610 Medicine & health, Plant Science, lcsh:Plant culture, 580 Plants (Botany), RNAseq, sporophyte development, mosses, UFSP13-7 Evolution in Action: From Genomes to Ecosystems, transcriptomics, 10121 Department of Systematic and Evolutionary Botany, 1110 Plant Science, lcsh:SB1-1110, 10211 Zurich-Basel Plant Science Center
Abstract

Understanding the molecular basis of morphological shifts is a fundamental question of evolutionary biology. New morphologies may arise through the birth/death of genes (gene gain/loss) or by reutilizing existing gene sets. Yet, the relative contribution of these two processes to radical morphological shifts is still poorly understood. Here, we use the model system of two mosses, Funaria hygrometrica and Physcomitrium (Physcomitrella) patens, to investigate the molecular mechanisms underlying contrasting sporophyte architectures. We used comparative analysis of time-series expression data for four stages of sporophyte development in both species to address this question in detail. We found that large-scale differences in sporophytic architecture are mainly governed by orthologous (i.e., shared) genes frequently experiencing temporal gene expression shifts between the two species. While the absolute number of species-specific genes expressed during sporophyte development is somewhat smaller, we observed a significant increase of their proportion in preferentially sporophyte expressed genes, suggesting a fundamental role in the sporophyte phase. However, further functional studies are necessary to determine their contribution to diverging sporophyte morphologies. Our results add to the growing set of studies suggesting that radical changes in morphology may rely on the heterochronic expression of conserved regulators.

Published
2020
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29. Anthoceros agrestis gametophyte DNA-seq

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, Jill C., 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, Szövényi, Péter, 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, Jill C., 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

Abstract

Anthoceros agrestis gametophyte DNA was sequenced and used for genome assembly.

Published
2020

30. Anthoceros RNA-seq

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, Jill C., 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, Szövényi, Péter, 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, Jill C., 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

Abstract

RNA-seq on gametophyte and sporophyte samples of Anthoceros agrestis.

Published
2020

31. 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, Jill C., 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, Szövényi, Péter, 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, Jill C., 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

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

32. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Author

Li, Fay-Wei; https://orcid.org/0000-0002-0076-0152, Nishiyama, Tomoaki; https://orcid.org/0000-0003-1279-7806, Waller, Manuel, Frangedakis, Eftychios, Keller, Jean; https://orcid.org/0000-0002-5198-0331, Li, Zheng, Fernandez-Pozo, Noe; https://orcid.org/0000-0002-6489-5566, Barker, Michael S; https://orcid.org/0000-0001-7173-1319, Bennett, Tom; https://orcid.org/0000-0003-1612-4019, Blázquez, Miguel A; https://orcid.org/0000-0001-5743-0448, Cheng, Shifeng, Cuming, Andrew C; https://orcid.org/0000-0003-2562-2052, de Vries, Jan; https://orcid.org/0000-0003-3507-5195, de Vries, Sophie; https://orcid.org/0000-0002-5267-8935, Delaux, Pierre-Marc; https://orcid.org/0000-0002-6211-157X, Diop, Issa S., Harrison, C Jill, Hauser, Duncan, Hernández-García, Jorge; https://orcid.org/0000-0003-2526-8639, Kirbis, Alexander, Meeks, John C, Monte, Isabel; https://orcid.org/0000-0002-7058-8343, Mutte, Sumanth K; https://orcid.org/0000-0003-3376-2354, Neubauer, Anna, Quandt, Dietmar, Robison, Tanner, Shimamura, Masaki, Rensing, Stefan A; https://orcid.org/0000-0002-0225-873X, Villarreal, Juan Carlos; https://orcid.org/0000-0002-0770-1446, Weijers, Dolf; https://orcid.org/0000-0003-4378-141X, Wicke, Susann, Wong, Gane K‐S; https://orcid.org/0000-0001-6108-5560, Sakakibara, Keiko, Szövényi, Péter; https://orcid.org/0000-0002-0324-4639, Li, Fay-Wei; https://orcid.org/0000-0002-0076-0152, Nishiyama, Tomoaki; https://orcid.org/0000-0003-1279-7806, Waller, Manuel, Frangedakis, Eftychios, Keller, Jean; https://orcid.org/0000-0002-5198-0331, Li, Zheng, Fernandez-Pozo, Noe; https://orcid.org/0000-0002-6489-5566, Barker, Michael S; https://orcid.org/0000-0001-7173-1319, Bennett, Tom; https://orcid.org/0000-0003-1612-4019, Blázquez, Miguel A; https://orcid.org/0000-0001-5743-0448, Cheng, Shifeng, Cuming, Andrew C; https://orcid.org/0000-0003-2562-2052, de Vries, Jan; https://orcid.org/0000-0003-3507-5195, de Vries, Sophie; https://orcid.org/0000-0002-5267-8935, Delaux, Pierre-Marc; https://orcid.org/0000-0002-6211-157X, Diop, Issa S., Harrison, C Jill, Hauser, Duncan, Hernández-García, Jorge; https://orcid.org/0000-0003-2526-8639, Kirbis, Alexander, Meeks, John C, Monte, Isabel; https://orcid.org/0000-0002-7058-8343, Mutte, Sumanth K; https://orcid.org/0000-0003-3376-2354, Neubauer, Anna, Quandt, Dietmar, Robison, Tanner, Shimamura, Masaki, Rensing, Stefan A; https://orcid.org/0000-0002-0225-873X, Villarreal, Juan Carlos; https://orcid.org/0000-0002-0770-1446, Weijers, Dolf; https://orcid.org/0000-0003-4378-141X, Wicke, Susann, Wong, Gane K‐S; https://orcid.org/0000-0001-6108-5560, Sakakibara, Keiko, and Szövényi, Péter; https://orcid.org/0000-0002-0324-4639

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

33. Immunogenicity and Safety of the BNT162b2 mRNA COVID-19 Vaccine Among Actively Treated Cancer Patients.

Author

Ligumsky, Hagai, Safadi, Esraa, Etan, Tal, Vaknin, Noam, Waller, Manuel, Croll, Assaf, Nikolaevski-Berlin, Alla, Greenberg, Inbal, Halperin, Tami, Wasserman, Asaf, Galazan, Lior, Arber, Nadir, and Wolf, Ido

Abstract

Background: Activity and safety of the SARS-CoV2 BNT162b2 vaccine in actively treated patients with solid tumors is currently unknown.Methods: We conducted a retrospective study of 326 patients with solid tumors treated with anti-cancer medications to determine the proportion of cancer patients with immunogenicity against SARS-CoV2, following two doses of the BNT162b2 vaccine. Control group was comprised of 164 vaccinated healthy adults. Anti-SARS-CoV-2 S IgG (Immunoglobulin G) antibodies (Abs) were measured, using level>50 AU/ml as cutoff for seropositivity. Adverse effects were collected using a questionnaire. All statistical tests were 2-sided.Results: Most patients (205, 62.9%) were treated with chemotherapy, either alone or with additional therapy, 55 (16.9%) were treated with immune checkpoint inhibitors (ICI) and 38 (11.7%) with targeted therapy alone, 28 (8.6%) received other combinations. The vaccine was well tolerated and no severe side effects were reported. Among patients with cancer 39 (11.9%) were seronegative, compared to 5 (3.0%) of the control group (P=0.001). Median IgG titers were statistically significant lower among patients with cancer compared to control (931 AU/ml vs. 2817 AU/ml, P=0.003). Seronegativity proportions were higher in the chemotherapy treated group (19, 18.8%) compared to the ICI-treated patients (5, 9.1%) and to those treated with targeted therapy (1, 2.6%) (P=0.02. Titers were also statistically significant different among treatment types (P=0.002).Conclusion: The BNT162b2 vaccine is safe and effective in actively treated patients with cancer. The relatively lower antibody titers and lower proportion of seropositive patients, especially among chemotherapy treated patients, call for continuing the use of personal protective measures in these patients, even following vaccination. [ABSTRACT FROM AUTHOR]

Published
2022
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34. CLAVATA was a genetic novelty for the morphological innovation of 3D growth in land plants

Author

Whitewoods, Chris D, Cammarata, Joseph, Nemec Venza, Zoe, Sang, Stephanie, Crook, Ashley D, et al, Waller, Manuel, Cuming, Andrew C, Szövényi, Peter, and University of Zurich

Subjects
UFSP13-7 Evolution in Action: From Genomes to Ecosystems, 10121 Department of Systematic and Evolutionary Botany, 1300 General Biochemistry, Genetics and Molecular Biology, General Biochemistry, Genetics and Molecular Biology, 1100 General Agricultural and Biological Sciences, 580 Plants (Botany), 10211 Zurich-Basel Plant Science Center, General Agricultural and Biological Sciences
Published
2018
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35. A pseudomolecule‐scale genome assembly of the liverwortMarchantia polymorpha

Author

Diop, Seydina I., primary, Subotic, Oliver, additional, Giraldo‐Fonseca, Alejandro, additional, Waller, Manuel, additional, Kirbis, Alexander, additional, Neubauer, Anna, additional, Potente, Giacomo, additional, Murray‐Watson, Rachel, additional, Boskovic, Filip, additional, Bont, Zoe, additional, Hock, Zsofia, additional, Payton, Adam C., additional, Duijsings, Daniël, additional, Pirovano, Walter, additional, Conti, Elena, additional, Grossniklaus, Ueli, additional, McDaniel, Stuart F., additional, and Szövényi, Péter, additional

Published
2019
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36. Evolution of the plant body plan

Author

Grossniklaus, Ueli; https://orcid.org/0000-0002-0522-8974, Grossniklaus, U ( Ueli ), Szövényi, Peter, Waller, Manuel, Kirbis, Alexander, Grossniklaus, Ueli; https://orcid.org/0000-0002-0522-8974, Grossniklaus, U ( Ueli ), Szövényi, Peter, Waller, Manuel, and Kirbis, Alexander

Published
2019

37. A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha.

Author

Diop, Seydina I., Subotic, Oliver, Giraldo‐Fonseca, Alejandro, Waller, Manuel, Kirbis, Alexander, Neubauer, Anna, Potente, Giacomo, Murray‐Watson, Rachel, Boskovic, Filip, Bont, Zoe, Hock, Zsofia, Payton, Adam C., Duijsings, Daniël, Pirovano, Walter, Conti, Elena, Grossniklaus, Ueli, McDaniel, Stuart F., and Szövényi, Péter

Subjects
PLANT genomes, BOTANY, RECOMBINANT DNA, LIVERWORTS, PHYSCOMITRELLA patens, VASCULAR plants
Abstract

Summary: Marchantia polymorpha has recently become a prime model for cellular, evo‐devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule‐scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high‐density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map‐based cloning, feasible. Significance Statement: Marchantia polymorpha has recently become a prime model for cellular, evolutionary‐developmental, synthetic biological, and evolutionary investigations with highly fragmented genomic resources (genome draft published in 2017; nearly 3000 scaffolds). To this end, we generated a pseudomolecule‐scale genome assembly of M. polymorpha, which will help to advance plant science by making comparative genome structure analysis and classical genetic mapping approaches feasible. [ABSTRACT FROM AUTHOR]

Published
2020
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38. Anthocerosgenomes 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

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 Anthoceroshornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthocerosgenomes 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 Anthocerosand upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a ChlamydomonasCCM 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
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41. Apomictic and Sexual Germline Development Differ with Respect to Cell Cycle, Transcriptional, Hormonal and Epigenetic Regulation

Author

Schmidt, Anja, Schmid, Marc W., Klostermeier, Ulrich C., Qi, Weihong, Guthörl, Daniela, Sailer, Christian, Waller, Manuel, Rosenstiel, Philip, and Grossniklaus, Ueli

Subjects
2. Zero hunger
Abstract

Seeds of flowering plants can be formed sexually or asexually through apomixis. Apomixis occurs in about 400 species and is of great interest for agriculture as it produces clonal offspring. It differs from sexual reproduction in three major aspects: (1) While the sexual megaspore mother cell (MMC) undergoes meiosis, the apomictic initial cell (AIC) omits or aborts meiosis (apomeiosis); (2) the unreduced egg cell of apomicts forms an embryo without fertilization (parthenogenesis); and (3) the formation of functional endosperm requires specific developmental adaptations. Currently, our knowledge about the gene regulatory programs underlying apomixis is scarce. We used the apomict Boechera gunnisoniana, a close relative of Arabidopsis thaliana, to investigate the transcriptional basis underlying apomeiosis and parthenogenesis. Here, we present the first comprehensive reference transcriptome for reproductive development in an apomict. To compare sexual and apomictic development at the cellular level, we used laser-assisted microdissection combined with microarray and RNA-Seq analyses. Conservation of enriched gene ontologies between the AIC and the MMC likely reflects functions of importance to germline initiation, illustrating the close developmental relationship of sexuality and apomixis. However, several regulatory pathways differ between sexual and apomictic germlines, including cell cycle control, hormonal pathways, epigenetic and transcriptional regulation. Enrichment of specific signal transduction pathways are a feature of the apomictic germline, as is spermidine metabolism, which is associated with somatic embryogenesis in various plants. Our study provides a comprehensive reference dataset for apomictic development and yields important new insights into the transcriptional basis underlying apomixis in relation to sexual reproduction., PLoS Genetics, 10 (7), ISSN:1553-7390, ISSN:1553-7404

42. 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
2. Zero hunger, Embryophyta, Anthocerotophyta, 15. Life on land, Biological Evolution, Life History Traits, Genome, Plant
Abstract

Funder: National Institute for Basic Biology (NIBB) Collaborative Research Program (13-710), Funder: The Forschungskredit of the University of Zurich The University Research Priority Program “Evolution in Action” of the University of Zurich The Georges and Antoine Claraz Foundation (Switzerland), Funder: Spanish Ministry of Science, Innovation and Universities (BFU2016-80621-P), Funder: The Georges and Antoine Claraz Foundation (Switzerland) The Research Priority Program “Evolution in Action” of the University of Zurich, Funder: Foundation of German Business (sdw), Georges and Antoine Claraz Foundation, URPP Evolution in Action of the University of Zurich, Funder: Special Grant for Innovation in Research Program of the Technical University of Dresden (Germany)., 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.

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