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3. 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

7. Origin and evolution of the nuclear auxin response system.

Author

Mutte, Sumanth K, Kato, Hirotaka, Rothfels, Carl, Melkonian, Michael, Wong, Gane Ka-Shu, and Weijers, Dolf

Subjects
Indoleacetic Acids, Plant Growth Regulators, Nuclear Proteins, Plant Proteins, Transcription Factors, Evolution, Molecular, Embryophyta, A. agrestis, C. richardii, M. polymorpha, P. patens, auxin, charophytes, evolutionary biology, genomics, plant biology, Evolution, Molecular, Biotechnology, Biochemistry and Cell Biology
Abstract

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here, we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

Published
2018

8. Design principles of a minimal auxin response system

Author

Kato, Hirotaka, Mutte, Sumanth K., Suzuki, Hidemasa, Crespo, Isidro, Das, Shubhajit, Radoeva, Tatyana, Fontana, Mattia, Yoshitake, Yoshihiro, Hainiwa, Emi, van den Berg, Willy, Lindhoud, Simon, Ishizaki, Kimitsune, Hohlbein, Johannes, Borst, Jan Willem, Boer, D. Roeland, Nishihama, Ryuichi, Kohchi, Takayuki, and Weijers, Dolf

Published
2020
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9. The birth of a giant : evolutionary insights into the origin of auxin responses in plants

Author

Carrillo-Carrasco, Vanessa Polet, Hernandez-Garcia, Jorge, Mutte, Sumanth K., Weijers, Dolf, Carrillo-Carrasco, Vanessa Polet, Hernandez-Garcia, Jorge, Mutte, Sumanth K., and Weijers, Dolf

Abstract

The plant signaling molecule auxin is present in multiple kingdoms of life. Since its discovery, a century of research has been focused on its action as a phytohormone. In land plants, auxin regulates growth and development through transcriptional and non-transcriptional programs. Some of the molecular mechanisms underlying these responses are well understood, mainly in Arabidopsis. Recently, the availability of genomic and transcriptomic data of green lineages, together with phylogenetic inference, has provided the basis to reconstruct the evolutionary history of some components involved in auxin biology. In this review, we follow the evolutionary trajectory that allowed auxin to become the “giant” of plant biology by focusing on bryophytes and streptophyte algae. We consider auxin biosynthesis, transport, physiological, and molecular responses, as well as evidence supporting the role of auxin as a chemical messenger for communication within ecosystems. Finally, we emphasize that functional validation of predicted orthologs will shed light on the conserved properties of auxin biology among streptophytes.

Published
2023

12. Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA

Author

Koopal, Balwina (author), Potocnik, Ana (author), Mutte, Sumanth K. (author), Aparicio Maldonado, C. (author), Lindhoud, Simon (author), Vervoort, Jacques J.M. (author), Brouns, S.J.J. (author), Swarts, Daan C. (author), Koopal, Balwina (author), Potocnik, Ana (author), Mutte, Sumanth K. (author), Aparicio Maldonado, C. (author), Lindhoud, Simon (author), Vervoort, Jacques J.M. (author), Brouns, S.J.J. (author), and Swarts, Daan C. (author)

Abstract

Argonaute proteins use single-stranded RNA or DNA guides to target complementary nucleic acids. This allows eukaryotic Argonaute proteins to mediate RNA interference and long prokaryotic Argonaute proteins to interfere with invading nucleic acids. The function and mechanisms of the phylogenetically distinct short prokaryotic Argonaute proteins remain poorly understood. We demonstrate that short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins form heterodimeric complexes. Upon guide RNA-mediated target DNA binding, four SPARTA heterodimers form oligomers in which TIR domain-mediated NAD(P)ase activity is unleashed. When expressed in Escherichia coli, SPARTA is activated in the presence of highly transcribed multicopy plasmid DNA, which causes cell death through NAD(P)+ depletion. This results in the removal of plasmid-invaded cells from bacterial cultures. Furthermore, we show that SPARTA can be repurposed for the programmable detection of DNA sequences. In conclusion, our work identifies SPARTA as a prokaryotic immune system that reduces cell viability upon RNA-guided detection of invading DNA., BN/Stan Brouns Lab

Published
2022
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13. A long look at short prokaryotic Argonautes

Author

Koopal, Balwina, Mutte, Sumanth K., Swarts, Daan C., Koopal, Balwina, Mutte, Sumanth K., and Swarts, Daan C.

Abstract

These files contain the data described in the manuscript "A long look at short prokaryotic Argonautes "., These files contain the data described in the manuscript "A long look at short prokaryotic Argonautes ".

Published
2022

15. SPARTA-related RNA and DNA

Author

Koopal, Balwina, Potocnik, Ana, Mutte, Sumanth K., Aparicio-Maldonado, Cristian, Lindhoud, Simon, Vervoort, Jacques J.M., Brouns, Stan J.J., Swarts, Daan C., Koopal, Balwina, Potocnik, Ana, Mutte, Sumanth K., Aparicio-Maldonado, Cristian, Lindhoud, Simon, Vervoort, Jacques J.M., Brouns, Stan J.J., and Swarts, Daan C.

Abstract

SPARTA-related small RNA, long RNA, and DNA Overall design: Total and small RNAseq data of total RNA from cells expressing SPARTA or co-purified with SPARTA complexes expressed in E. coli BL21(DE3), SPARTA-related small RNA, long RNA, and DNA Overall design: Total and small RNAseq data of total RNA from cells expressing SPARTA or co-purified with SPARTA complexes expressed in E. coli BL21(DE3)

Published
2021

16. 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

17. 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

18. 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

19. 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

20. Design principles of a minimal auxin response system

Author

Kato, Hirotaka, primary, Mutte, Sumanth K., additional, Suzuki, Hidemasa, additional, Crespo, Isidro, additional, Das, Shubhajit, additional, Radoeva, Tatyana, additional, Fontana, Mattia, additional, Yoshitake, Yoshihiro, additional, Hainiwa, Emi, additional, van den Berg, Willy, additional, Lindhoud, Simon, additional, Hohlbein, Johannes, additional, Borst, Jan Willem, additional, Boer, D. Roeland, additional, Nishihama, Ryuichi, additional, Kohchi, Takayuki, additional, and Weijers, Dolf, additional

Published
2019
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21. Design principles of a minimal auxin response system

Author

Kato, Hirotaka, Mutte, Sumanth K., Suzuki, Hidemasa, Crespo, Isidro, Das, Shubhajit, Radoeva, Tatyana, Fontana, Mattia, Yoshitake, Yoshihiro, Hainiwa, Emi, van den Berg, Willy, Lindhoud, Simon, Ishizaki, Kimitsune, Hohlbein, Johannes, Borst, Jan Willem, Boer, Roeland, Nishihama, Ryuichi, Kohchi, Takayuki, Weijers, Dolf, Kato, Hirotaka, Mutte, Sumanth K., Suzuki, Hidemasa, Crespo, Isidro, Das, Shubhajit, Radoeva, Tatyana, Fontana, Mattia, Yoshitake, Yoshihiro, Hainiwa, Emi, van den Berg, Willy, Lindhoud, Simon, Ishizaki, Kimitsune, Hohlbein, Johannes, Borst, Jan Willem, Boer, Roeland, Nishihama, Ryuichi, Kohchi, Takayuki, and Weijers, Dolf

Abstract

Transcriptome analysis using arf1 and arf3 mutants, to compare in vivo target specificity between Marchantia polymorpha ARF1 and ARF3 transcription factors, Transcriptome analysis using arf1 and arf3 mutants, to compare in vivo target specificity between Marchantia polymorpha ARF1 and ARF3 transcription factors

Published
2019

23. Origin and evolution of the nuclear auxin response system

Author

Mutte, Sumanth K., Kato, Hirotaka, Rothfels, Carl, Melkonian, Michael, Wong, Gane Ka-Shu, Weijers, Dolf, Mutte, Sumanth K., Kato, Hirotaka, Rothfels, Carl, Melkonian, Michael, Wong, Gane Ka-Shu, and Weijers, Dolf

Abstract

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here, we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

Published
2018

26. 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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27. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

Author

Dixit, Shalabh, primary, Kumar Biswal, Akshaya, additional, Min, Aye, additional, Henry, Amelia, additional, Oane, Rowena H., additional, Raorane, Manish L., additional, Longkumer, Toshisangba, additional, Pabuayon, Isaiah M., additional, Mutte, Sumanth K., additional, Vardarajan, Adithi R., additional, Miro, Berta, additional, Govindan, Ganesan, additional, Albano-Enriquez, Blesilda, additional, Pueffeld, Mandy, additional, Sreenivasulu, Nese, additional, Slamet-Loedin, Inez, additional, Sundarvelpandian, Kalaipandian, additional, Tsai, Yuan-Ching, additional, Raghuvanshi, Saurabh, additional, Hsing, Yue-Ie C., additional, Kumar, Arvind, additional, and Kohli, Ajay, additional

Published
2015
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28. 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.

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

Author

Isabel Monte, Pierre-Marc Delaux, Zheng Li, Dolf Weijers, Noe Fernandez-Pozo, Jan de Vries, Alexander Kirbis, Shifeng Cheng, Tanner A. Robison, Keiko Sakakibara, Jill C. Harrison, Sumanth K. Mutte, Péter Szövényi, Stefan A. Rensing, Tomoaki Nishiyama, Sophie de Vries, Masaki Shimamura, Tom Bennett, Miguel A. Blázquez, Eftychios Frangedakis, Jorge Hernández-García, Manuel Waller, Duncan A. Hauser, Juan Carlos Villarreal, John C. Meeks, Gane Ka-Shu Wong, Jean Keller, Dietmar Quandt, Michael S. Barker, Fay-Wei Li, Susann Wicke, Andrew C. Cuming, Issa S. Diop, Anna Neubauer, Boyce Thompson Institute [Ithaca], Cornell University [New York], Kanazawa University (KU), Universität Zürich [Zürich] = University of Zurich (UZH), Department of Plant, University of Oxford [Oxford], Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Orange Labs, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Campus de Teatinos s/n, Universidad de Málaga [Málaga] = University of Málaga [Málaga], Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Instituto de Biología Molecular y Celular de Plantas, Chinese Academy of Agricultural Sciences (CAAS), Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), University of Bristol [Bristol], Nees Institut for Plant Biodiversity, Rheinische Friedrich-Wilhelms-Universität Bonn, Faculty of Biology, University of Freiburg [Freiburg], Wageningen University and Research Centre (WUR), Department of Systematic and Evolutionary Botany, University of Vienna [Vienna], Li, Fay-Wei [0000-0002-0076-0152], Nishiyama, Tomoaki [0000-0003-1279-7806], Keller, Jean [0000-0002-5198-0331], Fernandez-Pozo, Noe [0000-0002-6489-5566], Barker, Michael S [0000-0001-7173-1319], Bennett, Tom [0000-0003-1612-4019], Blázquez, Miguel A [0000-0001-5743-0448], Cuming, Andrew C [0000-0003-2562-2052], de Vries, Jan [0000-0003-3507-5195], de Vries, Sophie [0000-0002-5267-8935], Delaux, Pierre-Marc [0000-0002-6211-157X], Hernández-García, Jorge [0000-0003-2526-8639], Monte, Isabel [0000-0002-7058-8343], Mutte, Sumanth K [0000-0003-3376-2354], Rensing, Stefan A [0000-0002-0225-873X], Villarreal, Juan Carlos [0000-0002-0770-1446], Weijers, Dolf [0000-0003-4378-141X], Wicke, Susann [0000-0001-5785-9500], Wong, Gane K-S [0000-0001-6108-5560], Sakakibara, Keiko [0000-0003-4420-9351], Szövényi, Péter [0000-0002-0324-4639], Apollo - University of Cambridge Repository, University of Zurich, and Li, Fay-Wei

Subjects
MESH: Genome, Plant, Crop and Pasture Production, 0106 biological sciences, Anthoceros, Evolution, [SDV]Life Sciences [q-bio], Lineage (evolution), Biochemie, Plant Biology, MESH: Biological Evolution, Anthocerotophyta, Plant Science, 580 Plants (Botany), Biology, Biochemistry, 01 natural sciences, Genome, Article, Pyrenoid, UFSP13-7 Evolution in Action: From Genomes to Ecosystems, Hornwort, 03 medical and health sciences, 1110 Plant Science, Genetics, Life Science, 10211 Zurich-Basel Plant Science Center, MESH: Anthocerotophyta / genetics, Clade, Life History Traits, 030304 developmental biology, 0303 health sciences, MESH: Life History Traits, Sporophyte, Plant, Genomics, 15. Life on land, biology.organism_classification, Biological Evolution, 10121 Department of Systematic and Evolutionary Botany, Evolutionary biology, Embryophyta, Bryophyte, MESH: Embryophyta / physiology, EPS, Plant sciences, Genome, Plant, 010606 plant biology & botany
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., Analyses of three high-quality genomes of Anthoceros hornworts place hornworts as a sister clade to the lineage including liverworts and mosses, and provide insights into the unique biological features of hornworts.

Published
2020
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