Projects per year
Organization profile
Organisation Profile
Our group is studying plant systems biology. We develop methods for combining different omics data sources and apply them in practise to answer biological questions regarding evolution, speciation, adaptation and host-microbe interactions in plants. Currently our main focus is the Betulaceae family, where we are establishing silver birch (Betula pendula) as the model species. In addition to silver birch we are also assembling the black alder genome (Alnus glutinosa).
Our work on host-microbe interactions has so far concentrated in the analysis of human gut microbiota. It forms a relatively closed ecosystem which can be quantified with 16S based techniques and metagenomic sequencing, and the host genome is very well annotated, making it suitable for a model ecosystem. In the following years the methodological approaches developed in this work will be applied to study plant-microbe interactions.
The group is part of Finnish Center of Excellence in Molecular Biology of Primary Producers.
International and National Collaboration
Publications and projects within past five years.
Profiles
Maja Ilievska
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Organismal and Evolutionary Biology Research Programme - Visiting scholar, Doctoral Student
- Doctoral Programme in Plant Sciences
Person: Visiting scholar, U1 Research and teaching staff, UH
Pezhman Safdari
- Research Centre for Ecological Change
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Organismal and Evolutionary Biology Research Programme - Doctoral Student
- Doctoral Programme in Plant Sciences
Person: U1 Research and teaching staff, UH
Omid Safronov
- Plant-Fungal Interactions Group
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Molecular and Integrative Biosciences Research Programme - Doctoral Student
- Doctoral Programme in Plant Sciences
Person: U1 Research and teaching staff, UH
Jarkko Salojärvi
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Viikki Plant Science Centre (ViPS)
- Organismal and Evolutionary Biology Research Programme - Academy Research Fellow
- Doctoral Programme in Plant Sciences - Supervisor for doctoral programme
Person: U3 Research and teaching staff, UH
Aleksia Vaattovaara
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Organismal and Evolutionary Biology Research Programme - Postdoctoral Researcher
Person: U2 Teaching and research staff
Projects
AngioPlast: Plastid genome evolution of angiosperms
Poczai, P., Hyvönen, J., Amiryousefi, A., Sablok, G. & He, X.
01/09/2017 → 30/09/2020
Project: Research project
SOLPHYLO: Phylogenetic Relationships and Organellar Genome Evolution in Solanaceae
Poczai, P., Hyvönen, J., Amiryousefi, A., Aubriot, X., Sablok, G., Särkinen, T., Knapp, S., Buerki, S., Syfert, M., He, X., Gagnon, E., Orejuela, A., Barboza, G., Baden, M. & van der Weerden, G. M.
Itä-Suomen yliopisto, Jyväskylän yliopisto, Uudenmaan liitto
01/09/2016 → 01/09/2020
Project: Research project
AMB: The phylogeny of ragweeds (genus Ambrosia, Asteraceae)
Poczai, P., Hyvönen, J., Amiryousefi, A., Sablok, G. & He, X.
15/03/2015 → 31/12/2020
Project: Research project
Three-year research grant / Mikael Niku 2016-2018: IMPACT OF FETAL INTESTINAL MICROBIOTA ON THE EARLY DEVELOPMENT OF THE IMMUNE SYSTEM
Niku, M., Pessa-Morikawa, T., Iivanainen, A., Satokari, R., Salojärvi, J., Soveri, T., Kahelin, M., Peltoniemi, O., Kareskoski, M., Alipour, M. & Husso, A.
Eläinlääketieteen tutkimuksen tukisäätiö, Suomen eläinlääketieteen säätiö, Suomen Kulttuurirahasto
01/01/2016 → 31/12/2019
Project: University of Helsinki Three-Year Research Project
Publications
CRK2 and C-terminal Phosphorylation of NADPH Oxidase RBOHD Regulate Reactive Oxygen Species Production in Arabidopsis
Kimura, S., Hunter, K., Vaahtera, L., Tran, C., Citterico, M., Vaattovaara, A., Rokka, A., Stolze, S. C., Harzen, A., Meißner, L., Wilneks, M. M. T., Hamann, T., Toyoga, M., Nakagami, H. & Wrzaczek, M., 8 Apr 2020, In : Plant Cell. 32, 4, p. 1063–1080 18 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access
ELIMAKI Locus Is Required for Vertical Proprioceptive Response in Birch Trees
Alonso Serra, J. A., Shi, X., Peaucelle, A., Rastas, P., Bourdon, M., Immanen, J., Takahashi, J., Koivula, H., Eswaran, G., Muranen, S. J., Help-Rinta-Rahko, H., Smolander, O-P., Su, C., Safronov, O., Gerber, L., Salojärvi, J., Hagqvist, R., Mähönen, A. P., Helariutta, Y. & Nieminen, K., 24 Feb 2020, In : Current Biology. 30, 4, p. 589-599 16 p.Research output: Contribution to journal › Article › Scientific › peer-review
PROTEIN PHOSPHATASE 2A-B 'gamma Controls Botrytis cinerea Resistance and Developmental Leaf Senescence
Durian, G., Rahikainen, M., Vuorinen, K., Gollan, P. J., Brosche, M., Salojarvi, J., Glawischnig, E., Winter, Z., Li, S., Noctor, G., Aro, E-M., Kangasjärvi, J., Overmyer, K., Burow, M. & Kangasjärvi, S., Feb 2020, In : Plant Physiology. 182, 2, p. 1161-1181 21 p.Research output: Contribution to journal › Article › Scientific › peer-review
The photoreceptor UVR8 mediates the perception of both UV-B and UV-A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes
Rai, N., O'Hara, A., Farkas, D., Safronov, O., Ratanasopa, K., Wang, F., Lindfors, A. V., Jenkins, G. I., Lehto, T., Salojärvi, J., Brosché, M., Strid, Å., Aphalo, P. J. & Morales, L. O., 24 Mar 2020, In : Plant, Cell and Environment. 15 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access
File
Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors
Shapiguzov, A., Vainonen, J., Hunter, K. A., Tossavainen, H. P. M., Tiwari, A., Järvi, S., Hellman, M. H., Aarabi, F., Alseekh, S., Wybouw, B., Van Der Kelen, K., Nikkanen, L., Krasensky-Wrzaczek, J., Sipari, N. H., Keinänen, M., Tyystjaervi, E., Rintamäki, E., De Rybel, B., Salojärvi, J. T., Van Breusegem, F. & 6 others, , 15 Feb 2019, In : eLife. 8, 35 p., e43284.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access
File
Activities
Plant and Animal Genomes Conference XXVI
Sitaram Rajaraman (Poster Presentation)15 Jan 2018
Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
Keystone Meeting: Plant Signaling: Molecular Pathways and Network Integration
Aleksia Vaattovaara (Poster Presentation)21 Jan 2018 → 24 Jan 2018
Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
Plant and Animal Genomes Conference XXVI
Sitaram Rajaraman (Speaker: Presenter)13 Jan 2018
Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
Population Genomics of Silver Birch
Jarkko Salojärvi (Speaker)13 Jan 2017 → 18 Jan 2017
Activity: Talk or presentation types › Oral presentation
Analysis of genomic sequencing data
Jarkko Salojärvi (Speaker)11 Dec 2017 → 13 Dec 2017
Activity: Talk or presentation types › Invited talk
Prizes
Global warming and boreal forest - a case study with the model species silver birch (Rauduskoivu)
Sitaram Rajaraman (Recipient), 26 Oct 2017
Prize: Prizes and awards
Press / Media
A simple software error corrected: bittersweet chloroplast genome becomes the model
Ali Amiryousefi, Jaakko Tapani Hyvönen & Péter Poczai
17/05/2018
1 item of Media coverage
Press/Media: Press / Media
A simple software error corrected: bittersweet chloroplast genome will become the model for annotations and nightshade comparative genomics
Ali Amiryousefi, Jaakko Tapani Hyvönen & Péter Poczai
14/05/2018
1 item of Media coverage
Press/Media: Press / Media