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4. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muñoz, Daniella Santos, Meidanis, João, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Métairon, Sylviane, Moine, Déborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, and Descombes, Patrick

Published
2024
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6. Transcriptional regulation of the CRK/DUF26 group of Receptor-like protein kinases by ozone and plant hormones in Arabidopsis

Author

Karpiński Stanisław, Robatzek Silke, Mersmann Sophia, Idänheimo Niina, Kangasjärvi Saijaliisa, Salojärvi Jarkko, Brosché Mikael, Wrzaczek Michael, Karpińska Barbara, and Kangasjärvi Jaakko

Subjects
Botany, QK1-989
Abstract

Abstract Background Plant Receptor-like/Pelle kinases (RLK) are a group of conserved signalling components that regulate developmental programs and responses to biotic and abiotic stresses. One of the largest RLK groups is formed by the Domain of Unknown Function 26 (DUF26) RLKs, also called Cysteine-rich Receptor-like Kinases (CRKs), which have been suggested to play important roles in the regulation of pathogen defence and programmed cell death. Despite the vast number of RLKs present in plants, however, only a few of them have been functionally characterized. Results We examined the transcriptional regulation of all Arabidopsis CRKs by ozone (O3), high light and pathogen/elicitor treatment - conditions known to induce the production of reactive oxygen species (ROS) in various subcellular compartments. Several CRKs were transcriptionally induced by exposure to O3 but not by light stress. O3 induces an extracellular oxidative burst, whilst light stress leads to ROS production in chloroplasts. Analysis of publicly available microarray data revealed that the transcriptional responses of the CRKs to O3 were very similar to responses to microbes or pathogen-associated molecular patterns (PAMPs). Several mutants altered in hormone biosynthesis or signalling showed changes in basal and O3-induced transcriptional responses. Conclusions Combining expression analysis from multiple treatments with mutants altered in hormone biosynthesis or signalling suggest a model in which O3 and salicylic acid (SA) activate separate signaling pathways that exhibit negative crosstalk. Although O3 is classified as an abiotic stress to plants, transcriptional profiling of CRKs showed strong similarities between the O3 and biotic stress responses.

Published
2010
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7. The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants

Author

Salojärvi Jarkko, Blomster Tiina, Vainonen Julia P, Wrzaczek Michael, Overmyer Kirk, Jaspers Pinja, Reddy Ramesha A, and Kangasjärvi Jaakko

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The SROs (SIMILAR TO RCD-ONE) are a group of plant-specific proteins which have important functions in stress adaptation and development. They contain the catalytic core of the poly(ADP-ribose) polymerase (PARP) domain and a C-terminal RST (RCD-SRO-TAF4) domain. In addition to these domains, several, but not all, SROs contain an N-terminal WWE domain. Results SROs are present in all analyzed land plants and sequence analysis differentiates between two structurally distinct groups; cryptogams and monocots possess only group I SROs whereas eudicots also contain group II. Group I SROs possess an N-terminal WWE domain (PS50918) but the WWE domain is lacking in group II SROs. Group I domain structure is widely represented in organisms as distant as humans (for example, HsPARP11). We propose a unified nomenclature for the SRO family. The SROs are able to interact with transcription factors through the C-terminal RST domain but themselves are generally not regulated at the transcriptional level. The most conserved feature of the SROs is the catalytic core of the poly(ADP-ribose) polymerase (PS51059) domain. However, bioinformatic analysis of the SRO PARP domain fold-structure and biochemical assays of AtRCD1 suggested that SROs do not possess ADP-ribosyl transferase activity. Conclusions The SROs are a highly conserved family of plant specific proteins. Sequence analysis of the RST domain implicates a highly preserved protein structure in that region. This might have implications for functional conservation. We suggest that, despite the presence of the catalytic core of the PARP domain, the SROs do not possess ADP-ribosyl transferase activity. Nevertheless, the function of SROs is critical for plants and might be related to transcription factor regulation and complex formation.

Published
2010
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8. Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars

Author

Hu, Guibing, Feng, Junting, Xiang, Xu, Wang, Jiabao, Salojärvi, Jarkko, Liu, Chengming, Wu, Zhenxian, Zhang, Jisen, Liang, Xinming, Jiang, Zide, Liu, Wei, Ou, Liangxi, Li, Jiawei, Fan, Guangyi, Mai, Yingxiao, Chen, Chengjie, Zhang, Xingtan, Zheng, Jiakun, Zhang, Yanqing, Peng, Hongxiang, Yao, Lixian, Wai, Ching Man, Luo, Xinping, Fu, Jiaxin, Tang, Haibao, Lan, Tianying, Lai, Biao, Sun, Jinhua, Wei, Yongzan, Li, Huanling, Chen, Jiezhen, Huang, Xuming, Yan, Qian, Liu, Xin, McHale, Leah K., Rolling, William, Guyot, Romain, Sankoff, David, Zheng, Chunfang, Albert, Victor A., Ming, Ray, Chen, Houbin, Xia, Rui, and Li, Jianguo

Published
2022
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9. Genomic insights into rapid speciation within the world’s largest tree genus Syzygium

Author

Low, Yee Wen, Rajaraman, Sitaram, Tomlin, Crystal M., Ahmad, Joffre Ali, Ardi, Wisnu H., Armstrong, Kate, Athen, Parusuraman, Berhaman, Ahmad, Bone, Ruth E., Cheek, Martin, Cho, Nicholas R. W., Choo, Le Min, Cowie, Ian D., Crayn, Darren, Fleck, Steven J., Ford, Andrew J., Forster, Paul I., Girmansyah, Deden, Goyder, David J., Gray, Bruce, Heatubun, Charlie D., Ibrahim, Ali, Ibrahim, Bazilah, Jayasinghe, Himesh D., Kalat, Muhammad Ariffin, Kathriarachchi, Hashendra S., Kintamani, Endang, Koh, Sin Lan, Lai, Joseph T. K., Lee, Serena M. L., Leong, Paul K. F., Lim, Wei Hao, Lum, Shawn K. Y., Mahyuni, Ridha, McDonald, William J. F., Metali, Faizah, Mustaqim, Wendy A., Naiki, Akiyo, Ngo, Kang Min, Niissalo, Matti, Ranasinghe, Subhani, Repin, Rimi, Rustiami, Himmah, Simbiak, Victor I., Sukri, Rahayu S., Sunarti, Siti, Trethowan, Liam A., Trias-Blasi, Anna, Vasconcelos, Thais N. C., Wanma, Jimmy F., Widodo, Pudji, Wijesundara, Douglas Siril A., Worboys, Stuart, Yap, Jing Wei, Yong, Kien Thai, Khew, Gillian S. W., Salojärvi, Jarkko, Michael, Todd P., Middleton, David J., Burslem, David F. R. P., Lindqvist, Charlotte, Lucas, Eve J., and Albert, Victor A.

Published
2022
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11. Complex Polyploids : Origins, Genomic Composition, and Role of Introgressed Alleles

Author

Leal, J Luis, Milesi, Pascal, Hodková, Eva, Zhou, Qiujie, James, Jennifer, Eklund, D Magnus, Pyhäjärvi, Tanja, Salojärvi, Jarkko, Lascoux, Martin, Leal, J Luis, Milesi, Pascal, Hodková, Eva, Zhou, Qiujie, James, Jennifer, Eklund, D Magnus, Pyhäjärvi, Tanja, Salojärvi, Jarkko, and Lascoux, Martin

Abstract

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid’s ancestral species, profoundly reshaping the polyploid’s genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000–188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilisfollowed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species’ range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

Published
2024
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13. Tipping Elements in the Human Intestinal Ecosystem

Author

Lahti, Leo, Salojärvi, Jarkko, Salonen, Anne, Scheffer, Marten, and de Vos, Willem M.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Recent studies show that the microbial communities inhabiting the human intestine can have profound impact on our well-being and health. However, we have limited understanding of the mechanisms that control this complex ecosystem. Based on a deep phylogenetic analysis of the intestinal microbiota in a thousand western adults we identified groups of bacteria that tend to be either nearly absent, or abundant in most individuals. The abundances of these bimodally distributed bacteria vary independently, and their contrasting alternative states are associated with host factors such as ageing and overweight. We propose that such bimodal groups represent independent tipping elements of the intestinal microbiota. These reflect the overall state of the intestinal ecosystem whose critical transitions can have profound health implications and diagnostic potential., Comment: 29 pages; 9 figures; 4 tables; preprint

Published
2014
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14. The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation

Author

Rendón-Anaya, Martha, Ibarra-Laclette, Enrique, Méndez-Bravo, Alfonso, Lan, Tianying, Zheng, Chunfang, Carretero-Paulet, Lorenzo, Perez-Torres, Claudia Anahí, Chacón-López, Alejandra, Hernandez-Guzmán, Gustavo, Chang, Tien-Hao, Farr, Kimberly M., Barbazuk, W. Brad, Chamala, Srikar, Mutwil, Marek, Shivhare, Devendra, Alvarez-Ponce, David, Mitter, Neena, Hayward, Alice, Fletcher, Stephen, Rozas, Julio, Gracia, Alejandro Sánchez, Kuhn, David, Barrientos-Priego, Alejandro F., Salojärvi, Jarkko, Librado, Pablo, Sankoff, David, Herrera-Estrella, Alfredo, Albert, Victor A., and Herrera-Estrella, Luis

Published
2019

15. Tissue-specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark

Author

Alonso-Serra, Juan, Safronov, Omid, Lim, Kean-Jin, Fraser-Miller, Sara J., Blokhina, Olga B., Campilho, Ana, Chong, Sun-Li, Fagerstedt, Kurt, Haavikko, Raisa, Helariutta, Ykä, Immanen, Juha, Kangasjärvi, Jaakko, Kauppila, Tiina J., Lehtonen, Mari, Ragni, Laura, Rajaraman, Sitaram, Räsänen, Riikka-Marjaana, Safdari, Pezhman, Tenkanen, Maija, Yli-Kauhaluoma, Jari T., Teeri, Teemu H., Strachan, Clare J., Nieminen, Kaisa, and Salojärvi, Jarkko

Published
2019

16. Tree architecture: A strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem

Author

Su, Chang, primary, Kokosza, Andrzej, additional, Xie, Xiaonan, additional, Pěnčík, Aleš, additional, Zhang, Youjun, additional, Raumonen, Pasi, additional, Shi, Xueping, additional, Muranen, Sampo, additional, Topcu, Melis Kucukoglu, additional, Immanen, Juha, additional, Hagqvist, Risto, additional, Safronov, Omid, additional, Alonso-Serra, Juan, additional, Eswaran, Gugan, additional, Venegas, Mirko Pavicic, additional, Ljung, Karin, additional, Ward, Sally, additional, Mähönen, Ari Pekka, additional, Himanen, Kristiina, additional, Salojärvi, Jarkko, additional, Fernie, Alisdair R., additional, Novák, Ondřej, additional, Leyser, Ottoline, additional, Pałubicki, Wojtek, additional, Helariutta, Ykä, additional, and Nieminen, Kaisa, additional

Published
2023
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17. Inference with Discriminative Posterior

Author

Salojärvi, Jarkko, Puolamäki, Kai, Savia, Eerika, and Kaski, Samuel

Subjects
Statistics - Machine Learning, Mathematics - Statistics Theory
Abstract

We study Bayesian discriminative inference given a model family $p(c,\x, \theta)$ that is assumed to contain all our prior information but still known to be incorrect. This falls in between "standard" Bayesian generative modeling and Bayesian regression, where the margin $p(\x,\theta)$ is known to be uninformative about $p(c|\x,\theta)$. We give an axiomatic proof that discriminative posterior is consistent for conditional inference; using the discriminative posterior is standard practice in classical Bayesian regression, but we show that it is theoretically justified for model families of joint densities as well. A practical benefit compared to Bayesian regression is that the standard methods of handling missing values in generative modeling can be extended into discriminative inference, which is useful if the amount of data is small. Compared to standard generative modeling, discriminative posterior results in better conditional inference if the model family is incorrect. If the model family contains also the true model, the discriminative posterior gives the same result as standard Bayesian generative modeling. Practical computation is done with Markov chain Monte Carlo., Comment: 28 pages, 3 figures, submitted to a journal

Published
2008

18. The Receptor-like Pseudokinase GHR1 Is Required for Stomatal Closure

Author

Sierla, Maija, Hõrak, Hanna, Overmyer, Kirk, Waszczak, Cezary, Yarmolinsky, Dmitry, Maierhofer, Tobias, Vainonen, Julia P., Salojärvi, Jarkko, Denessiouk, Konstantin, Laanemets, Kristiina, Tõldsepp, Kadri, Vahisalu, Triin, Gauthier, Adrien, Puukko, Tuomas, Paulin, Lars, Auvinen, Petri, Geiger, Dietmar, Hedrich, Rainer, Kollist, Hannes, and Kangasjärvi, Jaakko

Published
2018

19. The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, primary, Rambani, Aditi, additional, Yu, Zhe, additional, Guyot, Romain, additional, Strickler, Susan, additional, Lepelley, Maud, additional, Wang, Cui, additional, Rajaraman, Sitaram, additional, Rastas, Pasi, additional, Zheng, Chunfang, additional, Muñoz, Daniella Santos, additional, Meidanis, João, additional, Paschoal, Alexandre Rossi, additional, Bawin, Yves, additional, Krabbenhoft, Trevor, additional, Wang, Zhen Qin, additional, Fleck, Steven, additional, Aussel, Rudy, additional, Bellanger, Laurence, additional, Charpagne, Aline, additional, Fournier, Coralie, additional, Kassam, Mohamed, additional, Lefebvre, Gregory, additional, Métairon, Sylviane, additional, Moine, Déborah, additional, Rigoreau, Michel, additional, Stolte, Jens, additional, Hamon, Perla, additional, Couturon, Emmanuel, additional, Tranchant-Dubreuil, Christine, additional, Mukherjee, Minakshi, additional, Lan, Tianying, additional, Engelhardt, Jan, additional, Stadler, Peter, additional, De Lemos, Samara Mireza Correia, additional, Suzuki, Suzana Ivamoto, additional, Sumirat, Ucu, additional, Man, Wai Ching, additional, Dauchot, Nicolas, additional, Orozco-Arias, Simon, additional, Garavito, Andrea, additional, Kiwuka, Catherine, additional, Musoli, Pascal, additional, Nalukenge, Anne, additional, Guichoux, Erwan, additional, Reinout, Havinga, additional, Smit, Martin, additional, Carretero-Paulet, Lorenzo, additional, Filho, Oliveiro Guerreiro, additional, Braghini, Masako Toma, additional, Padilha, Lilian, additional, Sera, Gustavo Hiroshi, additional, Ruttink, Tom, additional, Henry, Robert, additional, Marraccini, Pierre, additional, Van de Peer, Yves, additional, Andrade, Alan, additional, Domingues, Douglas, additional, Giuliano, Giovanni, additional, Mueller, Lukas, additional, Pereira, Luiz Filipe, additional, Plaisance, Stephane, additional, Poncet, Valerie, additional, Rombauts, Stephane, additional, Sankoff, David, additional, Albert, Victor A., additional, Crouzillat, Dominique, additional, de Kochko, Alexandre, additional, and Descombes, Patrick, additional

Published
2023
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21. The genome and population genomics of allopolyploid Coffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muñoz, Daniella Santos, Meidanis, João, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Métairon, Sylviane, Moine, Déborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, and Descombes, Patrick

Abstract

Coffea arabica, an allotetraploid hybrid of Coffea eugenioidesand Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabicaaccession and modern representatives of its diploid progenitors, C. eugenioidesand C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Published
2024
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22. Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition

Author

Kootte, Ruud S., Levin, Evgeni, Salojärvi, Jarkko, Smits, Loek P., Hartstra, Annick V., Udayappan, Shanti D., Hermes, Gerben, Bouter, Kristien E., Koopen, Annefleur M., Holst, Jens J., Knop, Filip K., Blaak, Ellen E., Zhao, Jing, Smidt, Hauke, Harms, Amy C., Hankemeijer, Thomas, Bergman, Jacques J.G.H.M., Romijn, Hans A., Schaap, Frank G., Olde Damink, Steven W.M., Ackermans, Mariette T., Dallinga-Thie, Geesje M., Zoetendal, Erwin, de Vos, Willem M., Serlie, Mireille J., Stroes, Erik S.G., Groen, Albert K., and Nieuwdorp, Max

Published
2017
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23. Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Author

Salojärvi, Jarkko, Smolander, Olli-Pekka, Nieminen, Kaisa, Rajaraman, Sitaram, Safronov, Omid, Safdari, Pezhman, Lamminmäki, Airi, Immanen, Juha, Lan, Tianying, Tanskanen, Jaakko, Rastas, Pasi, Amiryousefi, Ali, Jayaprakash, Balamuralikrishna, Kammonen, Juhana I, Hagqvist, Risto, Eswaran, Gugan, Ahonen, Viivi Helena, Serra, Juan Alonso, Asiegbu, Fred O, de Dios Barajas-Lopez, Juan, Blande, Daniel, Blokhina, Olga, Blomster, Tiina, Broholm, Suvi, Brosché, Mikael, Cui, Fuqiang, Dardick, Chris, Ehonen, Sanna E, Elomaa, Paula, Escamez, Sacha, Fagerstedt, Kurt V, Fujii, Hiroaki, Gauthier, Adrien, Gollan, Peter J, Halimaa, Pauliina, Heino, Pekka I, Himanen, Kristiina, Hollender, Courtney, Kangasjärvi, Saijaliisa, Kauppinen, Leila, Kelleher, Colin T, Kontunen-Soppela, Sari, Koskinen, J Patrik, Kovalchuk, Andriy, Kärenlampi, Sirpa O, Kärkönen, Anna K, Lim, Kean-Jin, Leppälä, Johanna, Macpherson, Lee, Mikola, Juha, Mouhu, Katriina, Mähönen, Ari Pekka, Niinemets, Ülo, Oksanen, Elina, Overmyer, Kirk, Palva, E Tapio, Pazouki, Leila, Pennanen, Ville, Puhakainen, Tuula, Poczai, Péter, Possen, Boy J H M, Punkkinen, Matleena, Rahikainen, Moona M, Rousi, Matti, Ruonala, Raili, van der Schoot, Christiaan, Shapiguzov, Alexey, Sierla, Maija, Sipilä, Timo P, Sutela, Suvi, Teeri, Teemu H, Tervahauta, Arja I, Vaattovaara, Aleksia, Vahala, Jorma, Vetchinnikova, Lidia, Welling, Annikki, Wrzaczek, Michael, Xu, Enjun, Paulin, Lars G, Schulman, Alan H, Lascoux, Martin, Albert, Victor A, Auvinen, Petri, Helariutta, Ykä, and Kangasjärvi, Jaakko

Published
2019
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28. Tree architecture: A strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem.

Author

Chang Su, Kokosza, Andrzej, Xiaonan Xie, Pěnčík, Aleš, Youjun Zhang, Raumonen, Pasi, Xueping Shi, Muranen, Sampo, Topcu, Melis Kucukoglu, Immanen, Juha, Hagqvist, Risto, Safronov, Omid, Alonso-Serra, Juan, Eswaran, Gugan, Venegas, Mirko Pavicic, Ljung, Karin, Ward, Sally, Mähönen, Ari Pekka, Himanen, Kristiina, and Salojärvi, Jarkko

Subjects
AUXIN, EUROPEAN white birch, CONCENTRATION gradient, TREES, BIRCH
Abstract

Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture. [ABSTRACT FROM AUTHOR]

Published
2023
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33. On Discriminative Joint Density Modeling

Author

Salojärvi, Jarkko, Puolamäki, Kai, Kaski, Samuel, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Gama, João, editor, Camacho, Rui, editor, Brazdil, Pavel B., editor, Jorge, Alípio Mário, editor, and Torgo, Luís, editor

Published
2005
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34. Implicit Relevance Feedback from Eye Movements

Author

Salojärvi, Jarkko, Puolamäki, Kai, Kaski, Samuel, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Duch, Włodzisław, editor, Kacprzyk, Janusz, editor, Oja, Erkki, editor, and Zadrożny, Sławomir, editor

Published
2005
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36. Transfer of Intestinal Microbiota From Lean Donors Increases Insulin Sensitivity in Individuals With Metabolic Syndrome

Author

Vrieze, Anne, Van Nood, Els, Holleman, Frits, Salojärvi, Jarkko, Kootte, Ruud S., Bartelsman, Joep F.W.M., Dallinga–Thie, Geesje M., Ackermans, Mariette T., Serlie, Mireille J., Oozeer, Raish, Derrien, Muriel, Druesne, Anne, Van Hylckama Vlieg, Johan E.T., Bloks, Vincent W., Groen, Albert K., Heilig, Hans G.H.J., Zoetendal, Erwin G., Stroes, Erik S., de Vos, Willem M., Hoekstra, Joost B.L., and Nieuwdorp, Max

Published
2012
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37. Insights into bear evolution from a Pleistocene polar bear genome

Author

Lan, Tianying, primary, Leppälä, Kalle, additional, Tomlin, Crystal, additional, Talbot, Sandra L., additional, Sage, George K., additional, Farley, Sean D., additional, Shideler, Richard T., additional, Bachmann, Lutz, additional, Wiig, Øystein, additional, Albert, Victor A., additional, Salojärvi, Jarkko, additional, Mailund, Thomas, additional, Drautz-Moses, Daniela I., additional, Schuster, Stephan C., additional, Herrera-Estrella, Luis, additional, and Lindqvist, Charlotte, additional

Published
2022
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41. Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata

Author

Safdari, Pezhman, Höckerstedt, Layla, Brosche, Mikael, Salojärvi, Jarkko, Laine, Anna-Liisa, Organismal and Evolutionary Biology Research Programme, Bioinformatics for Molecular Biology and Genomics (BMBG), Biosciences, Plant Biology, Viikki Plant Science Centre (ViPS), Plant stress and natural variation, Doctoral school in biological, environmental and food sciences, and School of Biological Sciences

Subjects
expression profile, Phenotypic Variation, pathogen-imposed selection, phenotypic resistance diversity, natural host populations, 1181 Ecology, evolutionary biology, Biological sciences [Science], Pathogen-Imposed Selection, Plant Science, phenotypic variation, 11831 Plant biology, Original Research
Abstract

High levels of phenotypic variation in resistance appears to be nearly ubiquitous across natural host populations. Molecular processes contributing to this variation in nature are still poorly known, although theory predicts resistance to evolve at specific loci driven by pathogen-imposed selection. Nucleotide-binding leucine-rich repeat (NLR) genes play an important role in pathogen recognition, downstream defense responses and defense signaling. Identifying the natural variation in NLRs has the potential to increase our understanding of how NLR diversity is generated and maintained, and how to manage disease resistance. Here, we sequenced the transcriptomes of five different Plantago lanceolata genotypes when inoculated by the same strain of obligate fungal pathogen Podosphaera plantaginis. A de novo transcriptome assembly of RNA-sequencing data yielded 24,332 gene models with N50 value of 1,329 base pairs and gene space completeness of 66.5%. The gene expression data showed highly varying responses where each plant genotype demonstrated a unique expression profile in response to the pathogen, regardless of the resistance phenotype. Analysis on the conserved NB-ARC domain demonstrated a diverse NLR repertoire in P. lanceolata consistent with the high phenotypic resistance diversity in this species. We find evidence of selection generating diversity at some of the NLR loci. Jointly, our results demonstrate that phenotypic resistance diversity results from a crosstalk between different defense mechanisms. In conclusion, characterizing the architecture of resistance in natural host populations may shed unprecedented light on the potential of evolution to generate variation. Published version This work was funded by the Academy of Finland (334276) and the European Research Council Consolidator Grant RESISTANCE (724508) to A-LL, and the Academy of Finland (318288) to JS.

Published
2021

42. Insights into bear evolution from a Pleistocene polar bear genome

Author

Lan, Tianying, primary, Leppälä, Kalle, additional, Tomlin, Crystal, additional, Talbot, Sandra L., additional, Sage, George K., additional, Farley, Sean D., additional, Shideler, Richard T., additional, Bachmann, Lutz, additional, Wiig, Øystein, additional, Albert, Victor A., additional, Salojärvi, Jarkko, additional, Mailund, Thomas, additional, Drautz-Moses, Daniela I., additional, Schuster, Stephan C., additional, Herrera-Estrella, Luis, additional, and Lindqvist, Charlotte, additional

Published
2021
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43. Genomic insights into rapid speciation within the world’s largest tree genus

Author

Low, Yee Wen, primary, Rajaraman, Sitaram, additional, Tomlin, Crystal, additional, Ahmad, Joffre Ali, additional, Ardi, Wisnu, additional, Armstrong, Kate, additional, Athen, Parusuraman, additional, Berhaman, Ahmad, additional, Bone, Ruth, additional, Cheek, Martin, additional, Cho, Nicholas Rui Wen, additional, Choo, Le Min, additional, Cowie, Ian, additional, Crayn, Darren, additional, Fleck, Steve, additional, Ford, Andrew, additional, Forster, Paul, additional, Girmansyah, Deden, additional, Goyder, David, additional, Gray, Bruce, additional, Heatubun, Charlie, additional, Ibrahim, Ali, additional, Ibrahim, Bazilah, additional, Jayasinghe, Himesh, additional, Kalat, Muhammad Ariffin, additional, Kathriarachchi, Hashendra, additional, Kintamani, Endang, additional, Koh, Sin Lan, additional, Lai, Joseph Tuck Kwong, additional, Lee, Serena Mei Lynn, additional, Leong, Paul Kiam Fee, additional, Lim, Weihao, additional, Lum, Shawn Kaihekulani Yamauchi, additional, Mahyuni, Ridha, additional, McDonald, William, additional, Metali, Faizah, additional, Mustaqim, Wendy, additional, Naiki, Akiyo, additional, Ngo, Kang Min, additional, Niissalo, Matti, additional, Ranasinghe, Subhani, additional, Repin, Remi, additional, Rustiami, Himmah, additional, Simbiak, Victor, additional, Sukri, Rahayu, additional, Sunarti, Siti, additional, Trethowan, Liam, additional, Trias-Blasi, Anna, additional, Vasconcelos, Thais, additional, Wanma, Jimmy, additional, Widodo, Pudji, additional, Wijesundara, Douglas Siril, additional, Worboys, Stuart, additional, Yap, Jing Wei, additional, Yong, Kien Thai, additional, Khew, Gillian S.W., additional, Salojärvi, Jarkko, additional, Michael, Todd, additional, Middleton, David, additional, Burslem, David, additional, Lindqvist, Charlotte, additional, Lucas, Eve, additional, and Albert, Victor, additional

Published
2021
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