Projects per year
Organization 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
International and National Collaboration
Publications and projects within past five years.
Profiles
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Maja Ilievska
- Organismal and Evolutionary Biology Research Programme - Doctoral Researcher
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Doctoral Programme in Plant Sciences
Person: U1 Research and teaching staff, Doctoral Researcher, UH
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Omid Safronov
- Organismal and Evolutionary Biology Research Programme - Postdoctoral Researcher
- Plant-Fungal Interactions Group
- Bioinformatics for Molecular Biology and Genomics (BMBG)
Person: U2 Teaching and research staff, UH
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Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme - Academy Research Fellow
- Bioinformatics for Molecular Biology and Genomics (BMBG)
- Viikki Plant Science Centre (ViPS)
- Doctoral Programme in Plant Sciences - Supervisor for doctoral programme
Person: U3 Research and teaching staff, UH
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Aleksia Vaattovaara
- Department of Agricultural Sciences - Postdoctoral Researcher
- 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., Kangasjärvi, J., Mähönen, A. P., Hölttä, T., Pyhäjärvi, T. S., Salojärvi, J., Nieminen, K., Shapiguzov, A., Kucukoglu Topcu, M., Sierla, M., Waszczak, C. & Vaten, A.
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., Hytönen, T., Vaattovaara, A. & Mähönen, A. P.
01/05/2021 → 31/12/2021
Project: Research project
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AngioPlast: Plastid genome evolution of angiosperms
Poczai, P., Hyvönen, J., Amiryousefi, A., Sablok, G. & He, X.
01/09/2017 → 30/12/2021
Project: Research project
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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 → 01/09/2021
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., 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 Kulttuurirahasto, Suomen eläinlääketieteen säätiö
01/01/2016 → 31/12/2019
Project: University of Helsinki Three-Year Research Project
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Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences
Leal, J. L., Milesi, P., Salojärvi, J. & Lascoux, M., 18 Mar 2023, (E-pub ahead of print) In: Systematic Biology. 19 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access -
Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis
Cui, F., Ye, X., Li, X., Yang, Y., Hu, Z., Overmyer, K., Brosche, M., Yu, H. & Salojärvi, J., 11 Jul 2022, In: Plant communications. 3, 4, 19 p., 100307.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Genetic Diversity Analysis of Sapindus in China and Extraction of a Core Germplasm Collection Using EST-SSR Markers
Liu, J., Gao, S., Xu, Y., Wang, M., Ngiam, J. J., Rui Wen, N. C., Yi, J. J. J., Weng, X., Jia, L. & Salojarvi, J., 24 May 2022, In: Frontiers in plant science. 13, 11 p., 857993.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Genomic insights into rapid speciation within the world's largest tree genus Syzygium
Low, Y. W., Rajaraman, S., Tomlin, C. M., Ahmad, J. A., Ardi, W. H., Armstrong, K., Athen, P., Berhaman, A., Bone, R. E., Cheek, M., Cho, N. R. W., Choo, L. M., Cowie, I. D., Crayn, D., Fleck, S. J., Ford, A. J., Forster, P., Girmansyah, D., Goyder, D. J., Gray, B., & 43 others, 12 Sep 2022, In: Nature Communications. 13, 15 p., 5031.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Nonstop mRNAs generate a ground state of mitochondrial gene expression noise
Ng, K. Y., Bal, G. L., Richter, U., Safronov, O., Paulin, L., Dunn, C. D., Paavilainen, V. O., Richer, J., Newman, W. G., Taylor, R. W. & Battersby, B. J., 18 Nov 2022, In: Science Advances. 8, 46, 16 p., eabq5234.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile
Activities
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Plant and Animal Genomes Conference XXVI
Sitaram Rajaraman (Poster Presentation)
15 Jan 2018Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
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Keystone Meeting: Plant Signaling: Molecular Pathways and Network Integration
Aleksia Vaattovaara (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
Sitaram Rajaraman (Speaker: Presenter)
13 Jan 2018Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
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The adaptive landscape of silver birch illustrated by genome sequencing and population genomic analyses
Jarkko Salojärvi (Speaker)
1 Oct 2017 → 3 Oct 2017Activity: Talk or presentation types › Oral presentation
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Metagenomic analyses of the human gut microbiome reveal connections to the immune system
Jarkko Salojärvi (Pre-examiner)
1 Jan 2017 → 15 Jan 2017Activity: Examination types › Pre-examiner of doctoral thesis
Prizes
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Global warming and boreal forest - a case study with the model species silver birch (Rauduskoivu)
Rajaraman, Sitaram (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
Ali Amiryousefi, Jaakko Tapani Hyvönen & Péter Poczai
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
Ali Amiryousefi, Jaakko Tapani Hyvönen & Péter Poczai
14/05/2018
1 item of Media coverage
Press/Media: Press / Media