Publications
Selected Publications of the members of the Centre of Excellence in Tree Biology (TreeBio)
Selected Publications

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. (2020) ELIMAKI Locus Is Required for Vertical Proprioceptive Response in Birch Trees. Current Biology. 30, 589-599

Alonso-Serra, J., Safronov, O., Lim, K-J., Fraser-Miller, S.J., Blokhina, O.B., Campilho, A., Chong, S-L., Fagerstedt, K., Haavikko, R., Helariutta, Y., Immanen, J., Kangasjärvi, J., Kauppila, T.J., Lamminmäki, A., Lehtonen, M., Ragni, L., Rajaraman, S., Runeberg-Roos, P., Räsänen, R-M., Safdari, P., Tenkanen, M., Yli-Kauhaluoma, J.T., Teeri, T., Strachan, C., Nieminen, K., Salojärvi, J. (2019) Tissue-Specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark. New Phytologist 222, 1816-1831

Cervantes, S., Vuosku, J., & Pyhäjärvi, T. (2021) Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris. PeerJ 9, e11781

Fischer, U., Kucukoglu, M., Helariutta, Y., Bhalerao, RP. (2019) The Dynamics of Cambial Stem Cell Activity. Annual Review of Plant Biology 70, 293-319

Furuta, K. M., Yadav, S. R., Lehesranta, S., Belevich, I., Miyashima, S., Heo, J., Vaten, A., Lindgren, O., De Rybel, B., Van Isterdael, G., Somervuo, P., Lichtenberger, R., Rocha, R., Thitamadee, S., Tähtiharju, S., Auvinen, P., Beeckman, T., Jokitalo, E. & Helariutta, Y. (2014) Arabidopsis NAC45/86 direct sieve element morphogenesis culminating in enucleation. Science 345, 933-937

Hölttä, T., Mencuccini, M., Nikinmaa, E. (2009) Linking phloem function to structure: Analysis with a coupled xylem–phloem transport model. Journal of Theoretical Biology 259, 325-337

Hölttä, T., Lintunen, A., Chan, T., Mäkelä, A., & Nikinmaa, E. (2017) A steady-state stomatal model of balanced leaf gas exchange, hydraulics and maximal source–sink flux. Tree Physiology 37, 851–868

Hõrak, H., Sierla, M., Tõldsepp, K., Wang, C., Wang, Y-S., Nuhkat, M., Valk, E., Pechter, P., Merilo, E., Salojärvi, J., Overmyer, K., Loog, M., Brosché, M., Schroeder, J., Kangasjärvi, J. and Kollist, H. (2016) A dominant mutation in the HT1 kinase uncovers MAP kinases and GHR1 in CO2-induced stomatal closure. The Plant Cell 10, 2493-2509

Hu, G., Feng, J., Xiang, X., Wang, J., Salojärvi, J, Liu, Ch., Wu, Z., Zhang, J., Liang, X., Jiang, Z., Liu, W., Ou, L., Li, J., Fan, G., Mai, Y., Chen, Ch., Peng, H., Yao, L., Wai, Ch.M., Luo, X., Fu, J., Tang, H., Lan, T., Lai, B., Sun, J., Wei, Y., Li, H., Chen, J., Huang, X., Liu, X., McHale, L.K., Rolling, W., Guyot, R., Sankoff, D., Zheng, Ch., Albert, V.A., Ming, R., Chen, R., Xia, R., Li, J. (2022) Two divergent haplotypes from a highly heterozygous lychee genome point to independent domestication events for early and late-maturing cultivars. Nature Genetics 54, 73–83

Immanen, J., Nieminen, K., Smolander, O.P., Kojima, M., Alonso Serra, J., Koskinen, P., Zhang, J., Elo, A., Mähönen, A.P., Street, N., Bhalerao, R.P., Paulin, L., Auvinen, P., Sakakibara, H., Helariutta, Y. (2016) Cytokinin and auxin display distinct but interconnected distribution and signaling profiles to stimulate cambial activity. Current Biology 26, 1990-1997

Jyske, T., & Hölttä, T. (2015) Comparison of phloem and xylem hydraulic architecture in Picea abies stems. New Phytologist 205, 102-115

Kastally, C., Niskanen, A. K., Perry, A., Kujala, S. T., Avia, K., Cervantes, S., Haapanen M., Kesälahti, R., Kumpula, T. A., Mattila. T. M., Ojeda, D. I., Tyrmi, J. S., Wachowiak, W., Cavers, S., Kärkkäinen, K., Savolainen, O. & Pyhäjärvi, T. (2022) Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research. The Plant Journal. In Press

Kucukoglu, M., Chaabouni, S., Zheng, B., Mähönen, A.P., Helariutta, Y., Nilsson, O. (2020). Peptide encoding Populus CLV3/ESR-RELATED 47 (PttCLE47) promotes cambial development and secondary xylem formation in hybrid aspen. New Phytologist 226, 75-85

Kucukoglu, M., Nilsson, J., Zheng, B., Chaabouni, S., Nilsson, O. (2017) WUSCHEL-RELATED HOMEOBOX4 (WOX4)-like genes regulate cambial cell division activity and secondary growth in Populus trees. New Phytologist 215, 642-657

Kucukoglu, M., Nilsson, O. (2015) CLE peptide signaling in plants - the power of moving around. Physiologia Plantarum 155, 74-87

Lintunen, A., Paljakka, T., Salmon, Y., Dewar, R., Riikonen, A., & Hölttä, T. (2020) The influence of soil temperature and water content on belowground hydraulic conductance and leaf gas exchange in mature trees of three boreal species. Plant, Cell & Environment 43, 532-547

Lopez-Anido, CB., Vatén, A., Smoot, NK., Sharma, N., Guo, V., Gong, Y., Anleu Gil, MX., Weimer, AK., Bergmann, DC. (2021) Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf. Developmental Cell 56, 1043–55

Mähönen, A. P., ten Tusscher, K., Siligato, R., Smetana, O., Diaz-Trivino, S., Salojärvi, J. T., Wachsman, G., Prasad, K., Heidstra, R. & Scheres, B. (2014) PLETHORA gradient formation mechanism separates auxin responses. Nature 515, 125-129

Miyashima, S., Roszak, P., Sevilem, I., Toyokura, K., Blob, B., Heo, J., Mellor, N., Help-Rinta-Rahko, H., Otero, S., Smet, W., Boekschoten, M., Hooiveld, G., Hashimoto, K., Smetana, O., Siligato, R., Wallner, E-S., Mähönen, A. P., Kondo, Y., Melnyk, C. W., Greb, T., Nakajima, K., Sozzani, R., Bishopp, A., De Rybel, B., Helariutta, Y. (2019) Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Nature 565, 490-494

Nieminen, K., Immanen, J., Laxell, M., Kauppinen, L., Tarkowski, P., Dolezal, K., Tähtiharju, S., Elo, A.K., Decourteix, M., Ljung, K., Bhalerao, R., Keinonen, K., Albert, V.A., Helariutta, Y. (2008) Cytokinin signaling regulates cambial development in poplar. Proc. Natl. Acad. Sci. USA. 105, 20032-20037

Ojeda, D., Mattila, T.M., Ruttink, T., Kujala, S.T., Kärkkäinen, K., Verta, J.P., Pyhäjärvi, T. (2019) Utilization of tissue ploidy level variation in de novo transcriptome assembly of Pinus sylvestris. G3: Genes, Genomes, Genetics 9, 3409-3421

Pyhäjärvi, T., Kujala, ST., Savolainen, O. (2020) 275 years of forestry meets genomics in Pinus sylvestris. Evolutionary Applications 13, 11-30

Roszak, P., Heo, J., Blob, B., Toyokura, K., De Luis Balaguer, M. A., Lau, W., Hamey, F. K., Cirrone, J., Wang, X., Ursache, R., Tavares, H., Verstaen, K., Wendrich, J., Melnyk, C. W., Shasha, D., Ahnert, S., Saeys, Y., De Rybel, B., Heidstra, R., Scheres, B., Grossmann, G., Mähönen, A.P., Denninger, P., Göttgens, B., Sozzani, R., Birnbaum, KD., Helariutta, Y. (2021) Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. Science 374, eaba5531

Salmon, Y., Lintunen, A., Dayet, A., Chan, T., Dewar, R., Vesala, T., & Hölttä, T. (2020) Leaf carbon and water status control stomatal and non‐stomatal limitations of photosynthesis in trees. New Phytologist 226, 690-703. 

Salojärvi, J., Smolander, O-P., Nieminen, K., Rajaraman, S., Safronov, O., Safdari, P., Lamminmäki, A., Immanen, J., Lan, T., Tanskanen, J., Rastas, P., Amiryousefi, A., Jayaprakash, B., Kammonen, J. I., Hagqvist, R., Eswaran, G., Ahonen, V. H., Serra, J. A., Asiegbu, F. O., Barajas-Lopez, J. D. D., [...], Albert, V.A., Auvinen, P., Helariutta, Y.Kangasjarvi, J. (2017) Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nature Genetics 49, 904-912

Shapiguzov, A., B. Ingelsson, I. Samol, C. Andres, F. Kessler, J.D. Rochaix, A.V. Vener, and M. Goldschmidt-Clermont. (2010) The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the USA 107, 4782-7

Shapiguzov, A., Vainonen, J.P., Hunter, K., Tossavainen, H., Tiwari, A., Järvi, S., Hellman, M., Aarabi, F., Alseekh, S., Wybouw, B., Van Der Kelen, B., Nikkanen, L., Krasensky-Wrzaczek, J., Sipari, N., Keinänen, M., Tyystjärvi, E., Rintamäki, E., De Rybel, B., Salojärvi, J., Van Breusegem, F., Fernie, A.R., Brosché, M., Permi, P., Aro, E.-M., Wrzaczek, M., and Kangasjärvi, J. (2019) Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors. eLife 8, e43284

Shapiguzov, A., Vainonen, J.P., Wrzaczek, M., and Kangasjärvi, J. (2012) ROS-talk - how the apoplast, the chloroplast, and the nucleus get the message through. Frontiers in Plant Science 3, 292

Shapiguzov, A., L. Nikkanen, D. Fitzpatrick, J.P. Vainonen, A. Tiwari, R. Gossens, S. Alseekh, F. Aarabi, O. Blokhina, K. Panzarová, Z. Benedikty, E. Tyystjärvi, A. R. Fernie, M. Trtílek, E.-M. Aro, E. Rintamäki, Kangasjärvi, J. (2020) Dissecting the interaction of photosynthetic electron transfer with mitochondrial signalling and hypoxic response in the Arabidopsis rcd1 mutant. Philosophical Transactions of the Royal Society B 375, 20190413

Shapiguzov, A., X. Chai, G. Fucile, P. Longoni, L. Zhang, and J.D. Rochaix. (2016) Activation of the Stt7/STN7 Kinase through Dynamic Interactions with the Cytochrome b6f Complex. Plant Physiology 171, 82-92

Sierla, M., Hõrak, H., Overmyer, K., Waszczak, C., Yarmolinsky, D., Maierhofer, T., Denessiouk, K., Laanemets, K., Tõldsepp, K., Vahisalu, T., Gauthier, A., Salojärvi, J., Paulin, L., Auvinen, P., Geiger, D., Hedrich, R., Kollist, H. and Kangasjärvi, J. (2018) The receptor-like pseudokinase GHR1 is required for stomatal closure. The Plant Cell, 30, 2813–2837

Sierla, M., Rahikainen, M., Salojärvi, J., Kangasjärvi, J. and Kangasjärvi, S. (2013) Apoplastic and chloroplastic redox signaling networks in plant stress responses. Antioxidants and redox signalling. 18, 2220-2239

Sierla, M., Waszczak, C., Vahisalu, T. and Kangasjärvi, J. (2016) Reactive oxygen species in the regulation of stomatal movements. Plant Physiology 171, 1569-1580

Smetana, O., Mäkilä, R., Lyu, M., Amiryousefi, A., Rodriguez, F. S., Wu, M-F., Sole-Gil, A., Gavarron, M. L., Siligato, R., Miyashima, S., Roszak, P., Blomster, T., Reed, J. W., Broholm, S. & Mähönen, A. P. (2019) High levels of auxin signalling define the stem-cell organizer of the vascular cambium. Nature 565, 485-489

Tyrmi, J., Vuosku, J., Acosta, Li, Z., Sterck, L., Savolainen, O., Pyhäjärvi, T. (2020) Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting. G3: Genes, Genomes, Genetics 10, 2683-2696

Vahisalu, T., Kollist, H., Wang, Y-F., Nishimura, N., Chan, W-Y., Valerio, G., Lamminmäki, A., Brosche, M., Moldau, H., Desikan, R., Schroeder, J. I. & Kangasjärvi, J. (2008) SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling. Nature 452, 487-491

Vatén, A., Soyars, CL., Tarr, PT., Nimchuk, ZL., Bergmann, DC. (2018) Modulation of asymmetric division diversity through cytokinin and SPEECHLESS regulatory interactions in the Arabidopsis stomatal lineage. Developmental Cell 47, 53-66

Vaten, A., Dettmer, J., Wu, S., Stierhof, Y-D., Miyashima, S., Yadav, S. R., Roberts, C. J., Campilho, A., Bulone, V., Lichtenberger, R., Lehesranta, S., Mähonen, A. P., Kim, J-Y., Jokitalo, E., Sauer, N., Scheres, B., Nakajima, K., Carlsbecker, A., Gallagher, K. L. & Helariutta, Y. (2011) Callose Biosynthesis Regulates Symplastic Trafficking during Root Development. Developmental Cell 21, 1144-1155

Vatén, A., Bergmann, D.C. (2012). Mechanisms of stomatal development: an evolutionary view. EvoDevo 3, 11. 

Wang, X., Ye, L., Lyu, M., Ursache, R., Löytynoja, A. & Mähönen, A. P. (2020) An inducible genome editing system for plants. Nature Plants 6, 766–772

Waszczak, C., Vahisalu, T., Yarmolinsky, D., Sierla, M., Zamora, O., Leal Gavarrón, M., Carter, R., Carmody, M., Puukko, T., Sipari, N., Lamminmäki, A., Durner, J., Ernst, D., Paulin, L., Auvinen, P., Fleming, AJ., Salojärvi, J., Kollist, H., Kangasjärvi, J. (2019) Genetic screen to saturate guard cell signaling network reveals a role of GDP-L-fucose metabolism in stomatal closure. bioRxiv

Wrzaczek, M., Vainonen, J. P., Stael, S., Tsiatsiani, L., Help-Rinta-Rahko, H., Gauthier, A., Kaufholdt, D., Bollhöner, B., Lamminmäki, A., Staes, A., Gevaert, K., Tuominen, H., Van Breusegem, F., Helariutta, Y. Kangasjärvi, J. (2015) GRIM REAPER peptide binds to receptor kinase PRK5 to trigger cell death in Arabidopsis. EMBO Journal. 34, 55-66

Ye, L., Wang, X., Lyu, M., Siligato, R., Eswaran, G., Vainio, L., Blomster, T., Zhang, J. & Mähönen, A. P. (2021) Cytokinins initiate secondary growth in the Arabidopsis root through a set of LBD genes. Current Biology 31, 3365-3373

Zhang, J., Eswaran, G., Alonso-Serra, J., Kucukoglu, M., Xiang, J., Yang, W., Elo, A., Nieminen, K., Damén, T., Joung, JG., Yun, JY., Lee, JH., Ragni, L., Barbier de Reuille, P., Ahnert, SE., Lee, JY., Mähönen, AP., Helariutta, Y. (2019). Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots. Nature Plants 5, 1033-1042