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
Pezhman Safdari
- Research Centre for Ecological Change
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Doctoral Programme in Plant Sciences
Person: UH, Teaching and research personnel
Omid Safronov
- Plant-Fungal Interactions Group
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Plant ROS-Signalling
- Institute of Biotechnology - Doctoral Student
- Doctoral Programme in Plant Sciences
Person: UH, Teaching and research personnel
Jarkko Salojärvi
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Viikki Plant Science Centre (ViPS)
- Doctoral Programme in Plant Sciences - Supervisor for doctoral programme
Person: UH, Teaching and research personnel
Projects 2015 2020
AngioPlast: Plastid genome evolution of angiosperms
Poczai, P., Hyvönen, J. T., Amiryousefi, A., Sablok, G. & He, X.
01/09/2017 → 30/09/2020
Project: Research project › _Research
SOLPHYLO: Phylogenetic Relationships and Organellar Genome Evolution in Solanaceae
Poczai, P., Hyvönen, J. T., 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 › _Research
Three-year research grant / Mikael Niku 2016-2018: IMPACT OF FETAL INTESTINAL MICROBIOTA ON THE EARLY DEVELOPMENT OF THE IMMUNE SYSTEM
Niku, M. M., Pessa-Morikawa, T. I., Iivanainen, A. V., Satokari, R. M., Salojärvi, J. T., Soveri, T. T., Kahelin, M., Peltoniemi, O. A. T., Kareskoski, A. M., Alipour, M. J. & Husso, A. J.
Eläinlääketieteen tutkimuksen tukisäätiö, Suomen Kulttuurirahasto, Suomen eläinlääketieteen säätiö
01/01/2016 → 31/12/2019
Project: University of Helsinki Three-Year Research Project
AMB: The phylogeny of ragweeds (genus Ambrosia, Asteraceae)
Poczai, P., Hyvönen, J. T., Amiryousefi, A., Sablok, G. & He, X.
15/03/2015 → 31/12/2018
Project: Research project › _Research
Publications 2014 2019
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
High-throughput sequencing data and the impact of plant gene annotation quality
Vaattovaara, A. F. M., Leppälä, J. M., Salojärvi, J. T. & Wrzaczek, M. A., 1 Feb 2019, In : Journal of Experimental Botany. 70, 4, p. 1069-1076 8 p., ery43.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access
File
Mechanistic insights into the evolution of DUF26-containing proteins in land plants
Vaattovaara, A. F. M., Brandt, B., Rajaraman, S., Safronov, O., Veidenberg, A., Luklová, M., Kangasjärvi, J. S., Löytynoja, A. P., Hothorn, M., Salojärvi, J. T. & Wrzaczek, M. A., 8 Feb 2019, In : Communications Biology. 2, 56.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access
Sequencing the plastid genome of giant ragweed (Ambrosia trifida, Asteraceae) from a herbarium specimen
Sablok, G., Amiryousefi, A., He, X., Hyvönen, J. T. & Poczai, P., 28 Feb 2019, In : Frontiers in plant science. 10, 18 p., 218.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access
File
Tissue-specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark.
Alonso Serra, J. A., Safronov, O., Lim, K-J., Fraser-Miller, S., Blokhina, O. B., Campilho, A., Chong, S-L., Fagerstedt, K. V., Haavikko, R. H., Helariutta, Y. E., Immanen, J. J. M., Kangasjärvi, J. S., Kauppila, T. J., Lehtonen, M., Ragni, L., Rajaraman, S., Riikka-Marjaana, R., Safdari, P., Tenkanen, T. M., Yli-Kauhaluoma, J. T. & 4 others, 6 Feb 2019, In : New Phytologist.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access
Activities 2014 2018
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
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
The adaptive landscape of silver birch illustrated by genome sequencing and population genomic analyses
Jarkko Salojärvi (Speaker)1 Oct 2017 → 3 Oct 2017
Activity: Talk or presentation types › Oral presentation
Population Genomics of Silver Birch
Jarkko Salojärvi (Speaker)13 Jan 2017 → 18 Jan 2017
Activity: Talk or presentation types › Oral presentation
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