Projects per year
Organisation 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.
Fields of Science
- 1183 Plant biology, microbiology, virology
- 1181 Ecology, evolutionary biology
- 112 Statistics and probability
Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
Profiles
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Maja Ilievska
- Organismal and Evolutionary Biology Research Programme - Visiting scholar
- Doctoral Programme in Plant Sciences
- Bioinformatics for Molecular Biology and Genomics (BMBG)
Person: Visiting scholar, Doctoral Researcher, UH
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Omid Safronov
- Molecular and Integrative Biosciences Research Programme - Visiting scholar
- Plant-Fungal Interactions Group
- Bioinformatics for Molecular Biology and Genomics (BMBG)
Person: Visiting scholar, UH
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Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme - University Researcher
- Doctoral Programme in Plant Sciences - Supervisor for doctoral programme
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Viikki Plant Science Centre (ViPS)
Person: U3 Research and teaching staff, UH
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Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme - Postdoctoral Researcher
- Bioinformatics for Molecular Biology and Genomics (BMBG)
Person: U2 Teaching and research staff
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TreeBio: Centre of Excellence in Tree Biology
Helariutta, Y. (Principal Investigator), Kangasjärvi, J. (Co-Principal Investigator), Mähönen, A. P. (Co-Principal Investigator), Hölttä, T. (Participant), Pyhäjärvi, T. S. (Participant), Salojärvi, J. (Participant), Nieminen, K. (Participant), Shapiguzov, A. (Participant), Kucukoglu Topcu, M. (Participant), Sierla, M. (Participant), Waszczak, C. (Participant) & Vaten, A. (Participant)
01/01/2022 → 31/01/2029
Project: Research project
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Efficient nuclei isolation protocols for analysing chromatin level regulation of phenotypic variation in perennial plants
Pyhäjärvi, T. S. (Principal Investigator), Hytönen, T. (Co-Principal Investigator), Vaattovaara, A. (Participant) & Mähönen, A. P. (Other)
01/05/2021 → 31/12/2021
Project: Research project
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AngioPlast: Plastid genome evolution of angiosperms
Poczai, P. (Principal Investigator), Hyvönen, J. (Project manager), Amiryousefi, A. (Participant), Sablok, G. (Participant) & He, X. (Participant)
01/09/2017 → 30/12/2021
Project: Research project
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SOLPHYLO: Phylogenetic Relationships and Organellar Genome Evolution in Solanaceae
Poczai, P. (Principal Investigator), Hyvönen, J. (Project manager), Amiryousefi, A. (Participant), Aubriot, X. (Participant), Sablok, G. (Project manager), Särkinen, T. (Participant), Knapp, S. (Participant), Buerki, S. (Participant), Syfert, M. (Participant), He, X. (Participant), Gagnon, E. (Participant), Orejuela, A. (Participant), Barboza, G. (Project manager), Baden, M. (Project manager) & van der Weerden, G. M. (Project manager)
Uudenmaan liitto, Jyväskylän yliopisto, Itä-Suomen yliopisto
01/09/2016 → 01/09/2021
Project: Research project
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Three-year research grant / Mikael Niku 2016-2018: IMPACT OF FETAL INTESTINAL MICROBIOTA ON THE EARLY DEVELOPMENT OF THE IMMUNE SYSTEM
Niku, M. (Project manager), Pessa-Morikawa, T. (Participant), Iivanainen, A. (Participant), Satokari, R. (Participant), Salojärvi, J. (Participant), Soveri, T. (Participant), Kahelin, M. (Participant), Peltoniemi, O. (Participant), Kareskoski, M. (Participant), Alipour, M. (Participant) & Husso, A. (Participant)
Eläinlääketieteen tutkimuksen tukisäätiö, Suomen eläinlääketieteen säätiö, Suomen Kulttuurirahasto
01/01/2016 → 31/12/2019
Project: University of Helsinki Three-Year Research Project
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A Novel Pathosystem With the Model Plant Arabidopsis thaliana for Defining the Molecular Basis of Taphrina Infections
Auzane, A., Christita, M., Wang, K., Sipilä, T., Rajaraman, S., Eswaran, G., Kemppinen, J., de la Fuente, A., Bouwmeester, K., Auvinen, P., Paulin, L., Salojärvi, J., Sierla, M., Broche, M. & Overmyer, K., 10 Jun 2025, In: Environmental microbiology reports. 17, 3, 19 p., e70118.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Distinct post-harvest deterioration pathways caused by light vs dark storage of fresh-cut lettuce packed in modified atmosphere
Steensma, P., Widjaja, F., Rajaraman, S., Annala, L., Klami, A., Salojärvi, J., Lehtonen, M., Mikkonen, K. S. & Kangasjärvi, S., Nov 2025, In: Postharvest Biology and Technology. 229, 17 p., 113687.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Gene regulatory network analysis of silver birch reveals the ancestral state of secondary cell wall biosynthesis in core eudicots
Ilievska, M., Chong, S.-L., Lim, K.-J., Immanen, J., Nieminen, K., Maaheimo, H., Helariutta, Y., Wurman-Rodrich, J., Dupree, P., Ord, J., Tenkanen, M. & Salojarvi, J., Jun 2025, In: New Phytologist. 246, 5, p. 2059-2074 16 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Genetic diversity and adaptive evolutionary history of Sapindus in China: insights from whole-genome resequencing of 100 representative individuals
Liu, J., Zhao, G., Zheng, Y., Xu, Y., Wang, M., Li, L., Sun, C., He, Q., Apuli, R. P., Jong, J. J. Y., Ngiam, J. J., Vaulin, A., Tham, R. J. K., Jia, L., Chen, Z. & Salojärvi, J., Jul 2025, In: Plant biotechnology journal. 23, 7, p. 2485-2500 16 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
InDel variation and contraction of the Crepeat binding factor family contribute to cold sensitivity in Betula fujianensis
Zhuang, H., Lin, E., Xie, J., Jiang, M., Ni, F., Shi, S., Liu, M., Miao, S., Wei, M., Li, C., Liu, J., Liu, X., Hu, X., Wu, W., Salojärvi, J. T. & Huang, H.-H., Oct 2025, In: Plant Cell. 37, 10, 20 p., koaf216.Research output: Contribution to journal › Article › Scientific › peer-review
Activities
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Keystone Meeting: Plant Signaling: Molecular Pathways and Network Integration
Vaattovaara, A. (Poster Presentation)
21 Jan 2018 → 24 Jan 2018Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
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Plant and Animal Genomes Conference XXVI
Rajaraman, S. (Poster Presentation)
15 Jan 2018Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
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Plant and Animal Genomes Conference XXVI
Rajaraman, S. (Speaker: Presenter)
13 Jan 2018Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
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Story of silver birch
Salojärvi, J. (Speaker)
2 Nov 2017Activity: Talk or presentation types › Invited talk
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Analysis of genomic sequencing data
Salojärvi, J. (Speaker)
11 Dec 2017 → 13 Dec 2017Activity: Talk or presentation types › Invited talk
Prizes
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Global warming and boreal forest - a case study with the model species silver birch (Rauduskoivu)
Rajaraman, S. (Recipient), 26 Oct 2017
Prize: Prizes and awards
Press/Media
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A simple software error corrected: bittersweet chloroplast genome becomes the model
Amiryousefi, A., Hyvönen, J. T. & Poczai, P.
17/05/2018
1 item of Media coverage
Press/Media: Press / Media
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A simple software error corrected: bittersweet chloroplast genome will become the model for annotations and nightshade comparative genomics
Amiryousefi, A., Hyvönen, J. T. & Poczai, P.
14/05/2018
1 item of Media coverage
Press/Media: Press / Media