Characterising the Gene Regulatory Networks Governing Photosynthesis: From Basic Understanding to Targeted Engineering

Project Information

PHOTONET-C4

Grant agreement ID: 637765

DOI

10.3030/637765

Project closed

EC signature date 21 August 2015

Start date 1 November 2015

End date 31 October 2021

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 482 363,00

EU contribution

€ 1 482 363,00

Coordinated by

THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
United Kingdom

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (34)

Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench

Author(s): David Emms Steven Kelly
Published in: Genome Biology and Evolution, 2020, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evaa211

Conditional stomatal closure in a fern shares molecular features with flowering plant active stomatal responses

Author(s): Andrew Plackett David Emms Steven Kelly Alistair Hetherington Jane Langdale
Published in: Current Biology, 2021, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2021.08.008

Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off

Author(s): Jacques W Bouvier, David M Emms, Timothy Rhodes, Jai S Bolton, Amelia Brasnett, Alice Eddershaw, Jochem R Nielsen, Anastasia Unitt, Spencer M Whitney, Steven Kelly
Published in: Molecular Biology and Evolution, 2021, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab079

SHOOT: phylogenetic gene search and ortholog inference

Author(s): David Emms, Steven Kelly
Published in: Genome Biology, 2022, ISSN 1465-6906
Publisher: BioMed Central
DOI: 10.1186/s13059-022-02652-8

NO GAMETOPHORES 2 Is a Novel Regulator of the 2D to 3D Growth Transition in the Moss Physcomitrella patens

Author(s): Laura Moody Steven Kelly Roxaana Clayton Zoe Weeks David Emms Jane A.Langdale
Published in: Current Biology, 2021, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2020.10.077

Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles

Author(s): Rona Costello, David M Emms, Steven Kelly
Published in: Molecular Biology and Evolution, Issue 37/4, 2019, Page(s) 969-981, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msz275

Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data

Author(s): Basel Abu-Jamous, Steven Kelly
Published in: Genome Biology, Issue 19/1, 2018, ISSN 1474-7596
Publisher: BioMed Central
DOI: 10.1186/s13059-018-1536-8

The economics of organellar gene loss and endosymbiotic gene transfer

Author(s): Steven Kelly
Published in: Genome Biology, Issue 5, 2021, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1101/2020.10.01.322487

Installation of C4 photosynthetic pathway enzymes in rice using a single construct.

Author(s): Maria Ermakova; Stéphanie Arrivault; Rita Giuliani; Florence R. Danila; Hugo Alonso-Cantabrana; Hugo Alonso-Cantabrana; Daniela Vlad; Hirofumi Ishihara; Regina Feil; Manuela Guenther; Gian Luca Borghi; Sarah Covshoff; Martha Ludwig; Asaph B. Cousins; Jane A. Langdale; Steven L. Kelly; John E. Lunn; Mark Stitt; Susanne von Caemmerer; Robert T. Furbank
Published in: Plant Biotechnology Journal, Issue 32, 2021, ISSN 1467-7644
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/pbi.13487

The Quest for Orthologs benchmark service and consensus calls in 2020

Author(s): Altenhoff, Adrian M; Garrayo-Ventas, Javier; Cosentino, Salvatore; Emms, David; Glover, Natasha M; Hernández-Plaza, Ana; Nevers, Yannis; Sundesha, Vicky; Szklarczyk, Damian; Fernández, José M; Codó, Laia; for Orthologs Consortium, the Quest; Gelpi, Josep Ll; Huerta-Cepas, Jaime; Iwasaki, Wataru; Kelly, Steven; Lecompte, Odile; Muffato, Matthieu; Martin, Maria J; Capella-Gutierrez, Salvador;
Published in: Nucleic Acids Research, 48 (W1), Issue 29, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.3929/ethz-b-000425390

Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves

Author(s): Alexander J. Hetherington; Alexander J. Hetherington; David M. Emms; Steven L. Kelly; Liam Dolan; Liam Dolan
Published in: Scientific Reports, Vol 10, Iss 1, Pp 1-10 (2020), Issue 30, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1101/2019.12.16.878298

The Quest for Orthologs benchmark service and consensus calls in 2020

Author(s): Adrian M Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José M Fernández, Laia Codó, the Quest for Orthologs Consortium, Josep Ll Gelpi, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria J Martin, Salvador Capella-Gutierrez, Paul D Thomas, Erik
Published in: Nucleic Acids Research, Issue 48/W1, 2020, Page(s) W538-W545, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa308

Codon choice directs constitutive mRNA levels in trypanosomes

Author(s): de Freitas Nascimento, Janaina; Kelly, Steven; Sunter, Jack; Carrington, Mark
Published in: eLife, Issue 2, 2018, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.17863/CAM.23265

OMGene: mutual improvement of gene models through optimisation of evolutionary conservation

Author(s): Michael P. Dunne, Steven Kelly
Published in: BMC Genomics, Issue 19/1, 2018, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-018-4704-z

Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria

Author(s): Emily A. Seward, Steven Kelly
Published in: Genome Biology, Issue 19/1, 2018, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-018-1480-7

The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire

Author(s): Friederike Grosse-Holz, Steven Kelly, Svenja Blaskowski, Farnusch Kaschani, Markus Kaiser, Renier A.L. van der Hoorn
Published in: Plant Biotechnology Journal, Issue 16/5, 2018, Page(s) 1068-1084, ISSN 1467-7644
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/pbi.12852

The Amount of Nitrogen Used for Photosynthesis Modulates Molecular Evolution in Plants

Author(s): Steven Kelly
Published in: Molecular Biology and Evolution, Issue 35/7, 2018, Page(s) 1616-1625, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msy043

An Alternative Strategy for Trypanosome Survival in the Mammalian Bloodstream Revealed through Genome and Transcriptome Analysis of the Ubiquitous Bovine Parasite Trypanosoma (Megatrypanum) theileri

Author(s): Steven Kelly, Alasdair Ivens, G. Adam Mott, Ellis O’Neill, David Emms, Olivia Macleod, Paul Voorheis, Kevin Tyler, Matthew Clark, Jacqueline Matthews, Keith Matthews, Mark Carrington
Published in: Genome Biology and Evolution, Issue 9/8, 2017, Page(s) 2093-2109, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evx152

STRIDE: Species Tree Root Inference from Gene Duplication Events.

Author(s): Emms, DM; Kelly, S
Published in: Molecular Biology and Evolution, Issue 5, 2017, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1101/140020

Multiple mechanisms for enhanced plasmodesmata density in disparate subtypes of C4 grasses

Author(s): Florence R Danila, William Paul Quick, Rosemary G White, Steven Kelly, Susanne von Caemmerer, Robert T Furbank
Published in: Journal of Experimental Botany, Issue 69/5, 2018, Page(s) 1135-1145, ISSN 0022-0957
Publisher: Oxford University Press
DOI: 10.1093/jxb/erx456

The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land

Author(s): Bruno Catarino, Alexander J. Hetherington, David M. Emms, Steven Kelly, Liam Dolan
Published in: Molecular Biology and Evolution, Issue 33/11, 2016, Page(s) 2815-2819, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw155

The Mechanism Forming the Cell Surface of Tip-Growing Rooting Cells Is Conserved among Land Plants

Author(s): Suvi Honkanen, Victor A.S. Jones, Giulia Morieri, Clement Champion, Alexander J. Hetherington, Steve Kelly, Hélène Proust, Denis Saint-Marcoux, Helen Prescott, Liam Dolan
Published in: Current Biology, Issue 26/23, 2016, Page(s) 3238-3244, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2016.09.062

Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms

Author(s): Emily A. Seward, Steven Kelly
Published in: Genome Biology, Issue 17/1, 2016, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-016-1087-9

Simulating topological domains in human chromosomes with a fitting-free model

Author(s): C. A. Brackley, D. Michieletto, F. Mouvet, J. Johnson, S. Kelly, P. R. Cook, D. Marenduzzo
Published in: Nucleus, Issue 7/5, 2016, Page(s) 453-461, ISSN 1949-1034
Publisher: Landes Bioscience
DOI: 10.1080/19491034.2016.1239684

Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species

Author(s): David M. Emms, Sarah Covshoff, Julian M. Hibberd, Steven Kelly
Published in: Molecular Biology and Evolution, Issue 33/7, 2016, Page(s) 1796-1806, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw057

TransRate: reference-free quality assessment of de novo transcriptome assemblies

Author(s): Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian M. Hibberd, Steven Kelly
Published in: Genome Research, Issue 26/8, 2016, Page(s) 1134-1144, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.196469.115

Engineering biosynthesis of high-value compounds in photosynthetic organisms

Author(s): Ellis C. O’Neill, Steven Kelly
Published in: Critical Reviews in Biotechnology, 2016, Page(s) 1-24, ISSN 0738-8551
Publisher: Taylor & Francis
DOI: 10.1080/07388551.2016.1237467

OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations

Author(s): Michael P. Dunne, Steven Kelly
Published in: BMC Genomics, Issue 18/1, 2017, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-017-3771-x

OrthoFinder: phylogenetic orthology inference for comparative genomics

Author(s): David M. Emms, Steven Kelly
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-7596
Publisher: BioMed Central
DOI: 10.1186/s13059-019-1832-y

Subdivision of Light Signaling Networks Contributes to Partitioning of C 4 Photosynthesis

Author(s): Ross-W. Hendron, Steven Kelly
Published in: Plant Physiology, Issue 182/3, 2020, Page(s) 1297-1309, ISSN 0032-0889
Publisher: American Society of Plant Biologists
DOI: 10.1104/pp.19.01053

Transcriptome, proteome and draft genome of Euglena gracilis

Author(s): ThankGod E. Ebenezer, Martin Zoltner, Alana Burrell, Anna Nenarokova, Anna M. G. Novák Vanclová, Binod Prasad, Petr Soukal, Carlos Santana-Molina, Ellis O’Neill, Nerissa N. Nankissoor, Nithya Vadakedath, Viktor Daiker, Samson Obado, Sara Silva-Pereira, Andrew P. Jackson, Damien P. Devos, Julius Lukeš, Michael Lebert, Sue Vaughan, Vladimίr Hampl, Mark Carrington, Michael L. Ginger, Joel B. Da
Published in: BMC Biology, Issue 17/1, 2019, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-019-0626-8

Codon choice directs constitutive mRNA levels in trypanosomes.

Author(s): Janaina de Freitas Nascimento; Steven Kelly; Jack Sunter; Mark Carrington
Published in: eLife, Issue 19, 2018, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.32467

Transcriptional control of photosynthetic capacity: conservation and divergence from Arabidopsis to rice

Author(s): Peng Wang; Ross-William Hendron; Steven L. Kelly
Published in: New Phytologist, Issue 20, 2017, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.14682

Multiple Metabolic Innovations and Losses Are Associated with Major Transitions in Land Plant Evolution

Author(s): Naomi Cannell, David M. Emms, Alexander J. Hetherington, John MacKay, Steven Kelly, Liam Dolan, Lee J. Sweetlove
Published in: Current Biology, Issue 30/10, 2020, Page(s) 1783-1800.e11, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2020.02.086