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2. Advanced Real-Time Monitoring System for Marine Net Pens: Integrating Sensors, GPRS, GPS, and IoT with Embedded Systems

Author

Panda, Sayantan, Narayanamoorthi, R., Dhanalakshmi, Samiappan, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Sharma, Devendra Kumar, editor, Peng, Sheng-Lung, editor, Sharma, Rohit, editor, and Jeon, Gwanggil, editor

Published
2024
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4. Parallel evolution of cannabinoid biosynthesis

Author

Berman, Paula, de Haro, Luis Alejandro, Jozwiak, Adam, Panda, Sayantan, Pinkas, Zoe, Dong, Younghui, Cveticanin, Jelena, Barbole, Ranjit, Livne, Rotem, Scherf, Tali, Shimoni, Eyal, Levin-Zaidman, Smadar, Dezorella, Nili, Petrovich-Kopitman, Ekaterina, Meir, Sagit, Rogachev, Ilana, Sonawane, Prashant D., and Aharoni, Asaph

Published
2023
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14. 2‐oxoglutarate‐dependent dioxygenases drive expansion of steroidal alkaloid structural diversity in the genus Solanum

Author

Sonawane, Prashant D., primary, Jozwiak, Adam, additional, Barbole, Ranjit, additional, Panda, Sayantan, additional, Abebie, Bekele, additional, Kazachkova, Yana, additional, Gharat, Sachin A., additional, Ramot, Ofir, additional, Unger, Tamar, additional, Wizler, Guy, additional, Meir, Sagit, additional, Rogachev, Ilana, additional, Doron‐Faigenboim, Adi, additional, Petreikov, Marina, additional, Schaffer, Arthur, additional, Giri, Ashok P., additional, Scherf, Tali, additional, and Aharoni, Asaph, additional

Published
2023
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16. Pathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases

Author

Cárdenas, Pablo D., Sonawane, Prashant D., Heinig, Uwe, Jozwiak, Adam, Panda, Sayantan, Abebie, Bekele, Kazachkova, Yana, Pliner, Margarita, Unger, Tamar, Wolf, Dalia, Ofner, Itai, Vilaprinyo, Ester, Meir, Sagit, Davydov, Olga, Gal-on, Amit, Burdman, Saul, Giri, Ashok, Zamir, Dani, Scherf, Tali, Szymanski, Jedrzej, Rogachev, Ilana, and Aharoni, Asaph

Published
2019
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18. 2‐oxoglutarate‐dependent dioxygenases drive expansion of steroidal alkaloid structural diversity in the genus Solanum

Author

Sonawane, Prashant D., primary, Jozwiak, Adam, additional, Barbole, Ranjit, additional, Panda, Sayantan, additional, Abebie, Bekele, additional, Kazachkova, Yana, additional, Gharat, Sachin A., additional, Ramot, Ofir, additional, Unger, Tamar, additional, Wizler, Guy, additional, Meir, Sagit, additional, Rogachev, Ilana, additional, Doron‐Faigenboim, Adi, additional, Petreikov, Marina, additional, Schaffer, Arthur, additional, Giri, Ashok P., additional, Scherf, Tali, additional, and Aharoni, Asaph, additional

Published
2022
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19. Uncovering Pathways Highly Correlated to NUE through a Combined Metabolomics and Transcriptomics Approach in Eggplant

Author

Mauceri, Antonio, primary, Aci, Meriem Miyassa, additional, Toppino, Laura, additional, Panda, Sayantan, additional, Meir, Sagit, additional, Mercati, Francesco, additional, Araniti, Fabrizio, additional, Lupini, Antonio, additional, Panuccio, Maria Rosaria, additional, Rotino, Giuseppe Leonardo, additional, Aharoni, Asaph, additional, Abenavoli, Maria Rosa, additional, and Sunseri, Francesco, additional

Published
2022
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20. A cellulose synthase-like protein governs the biosynthesis of Solanum alkaloids.

Author

Jozwiak, Adam, Panda, Sayantan, Akiyama, Ryota, Ayano Yoneda, Naoyuki Umemoto, Kazuki Saito, Shuhei Yasumoto, Toshiya Muranaka, Gharat, Sachin A., Kazachkova, Yana, Yonghui Dong, Arava, Shlomy, Goliand, Inna, Nevo, Reinat, Rogachev, Ilana, Meir, Sagit, Masaharu Mizutani, and Aharoni, Asaph

Subjects
*CELLULOSE synthase, *PROTEIN synthesis, *SOLANUM, *CELLULOSE, *METABOLITES, *MULTIENZYME complexes
Abstract

The article presents a study which identified GLYCO-ALKALOID METABOLISM15 (GAME15), a cellulose synthase-like M protein, as the so-called missing link in SGA biosynthesis. Topics discussed include finding on the localization of GAME15, effect of silencing GAME15 in tomato and potato, and importance of GAME15 for the biosynthesis of SGAs in Solanaceae plants.

Published
2024
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21. Steroidal alkaloids defence metabolism and plant growth are modulated by the joint action of gibberellin and jasmonate signalling

Author

Panda, Sayantan, primary, Jozwiak, Adam, additional, Sonawane, Prashant D., additional, Szymanski, Jedrzej, additional, Kazachkova, Yana, additional, Vainer, Andrii, additional, Vasuki Kilambi, Himabindu, additional, Almekias‐Siegl, Efrat, additional, Dikaya, Varvara, additional, Bocobza, Samuel, additional, Shohat, Hagai, additional, Meir, Sagit, additional, Wizler, Guy, additional, Giri, Ashok P., additional, Schuurink, Robert, additional, Weiss, David, additional, Yasuor, Hagai, additional, Kamble, Avinash, additional, and Aharoni, Asaph, additional

Published
2021
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26. Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response

Author

European Commission, European Research Council, Israel Science Foundation, Helmsley Charitable Trust, Jeanne and Joseph Nissim Foundation for Life Sciences Research, Szymański, Jędrzej, Bocobza, Samuel, Panda, Sayantan, Sonawane, Prashant, Cárdenas, Pablo D., Lashbrooke, Justin, Kamble, Avinash, Shahaf, Nir, Meir, Sagit, Bovy, Arnaud, Beekwilder, Jules, Tikunov, Yury, Romero, Irene, Zamir, Dani, Rogachev, Ilana, Aharoni, Asaph, European Commission, European Research Council, Israel Science Foundation, Helmsley Charitable Trust, Jeanne and Joseph Nissim Foundation for Life Sciences Research, Szymański, Jędrzej, Bocobza, Samuel, Panda, Sayantan, Sonawane, Prashant, Cárdenas, Pablo D., Lashbrooke, Justin, Kamble, Avinash, Shahaf, Nir, Meir, Sagit, Bovy, Arnaud, Beekwilder, Jules, Tikunov, Yury, Romero, Irene, Zamir, Dani, Rogachev, Ilana, and Aharoni, Asaph

Abstract

Wild tomato species represent a rich gene pool for numerous desirable traits lost during domestication. Here, we exploited an introgression population representing wild desert-adapted species and a domesticated cultivar to establish the genetic basis of gene expression and chemical variation accompanying the transfer of wild-species-associated fruit traits. Transcriptome and metabolome analysis of 580 lines coupled to pathogen sensitivity assays resulted in the identification of genomic loci associated with levels of hundreds of transcripts and metabolites. These associations occurred in hotspots representing coordinated perturbation of metabolic pathways and ripening-related processes. Here, we identify components of the Solanum alkaloid pathway, as well as genes and metabolites involved in pathogen defense and linking fungal resistance with changes in the fruit ripening regulatory network. Our results outline a framework for understanding metabolism and pathogen resistance during tomato fruit ripening and provide insights into key fruit quality traits.

Published
2020

27. A Multimodal Study of Wild Tomato Species Introgressions Unravels the Genetic Basis of Transcriptome and Metabolome Variation in Important Fruit Traits

Author

Szymański, Jędrzej, Bocobza, S.E., Panda, Sayantan, Sonawane, Prashant, Cardenas, Pablo D., Lashbrooke, Justin, Kamble, Avinash, Shahaf, Nir, Meir, Sagit, Bovy, Arnaud, Beekwilder, Jules, Tikunov, Yury, Romero de la Fuente, Irene, Zamir, Dani, Rogachev, Ilana, Aharoni, Asaph, Szymański, Jędrzej, Bocobza, S.E., Panda, Sayantan, Sonawane, Prashant, Cardenas, Pablo D., Lashbrooke, Justin, Kamble, Avinash, Shahaf, Nir, Meir, Sagit, Bovy, Arnaud, Beekwilder, Jules, Tikunov, Yury, Romero de la Fuente, Irene, Zamir, Dani, Rogachev, Ilana, and Aharoni, Asaph

Abstract

Here, we report RNAseq data from a Solanum lycopersicum-pennellii introgression population (IL) and a backcross introgression population (BIL), to establish the genetic basis of gene expression and chemical variation accompanying transfer of wild species-associated fruit traits. Transcriptome analysis of these lines resulted in the identification of genomic loci significantly linked with levels of hundreds of transcripts and metabolites. These associations occurred in functionally coherent hotspots that represent coordinated perturbation of metabolic pathways and ripening-related processes. We demonstrated the efficacy of our approach by discovering yet undisclosed components of the renowned Solanum alkaloids pathway and moreover, showing that fruit fungal resistance is associated with changes in the ripening regulatory network.

Published
2020

28. Analysis of Wild Tomato Introgression Lines Elucidates the Genetic Basis of Metabolome Variation in a Ripening Tomato Fruit

Author

Szymanski, Jedrzej, Bocobza, Samuel, Shahaf, Nir, Meir, Sagit, Rogachev, Ilana, Aharoni, Asaph, Panda, Sayantan, Sonawane, Prashant, Cárdenas, Pablo D., Lashbrooke, Justin, Kamble, Avinash, Bovy, Arnauld, Beekwilder, Jules, Tikunov, Yury, Romero de la Fuente, Irene, Zamir, Dani, Szymanski, Jedrzej, Bocobza, Samuel, Shahaf, Nir, Meir, Sagit, Rogachev, Ilana, Aharoni, Asaph, Panda, Sayantan, Sonawane, Prashant, Cárdenas, Pablo D., Lashbrooke, Justin, Kamble, Avinash, Bovy, Arnauld, Beekwilder, Jules, Tikunov, Yury, Romero de la Fuente, Irene, and Zamir, Dani

Abstract

LC-MS analysis of the Introgression Lines (ILs; Eshed & Zamir 1995) and Backcrossed Inbred Lines (BILs; Ofner et al. 2016) developped from the wild Peruvian accession of Solanum pennellii in the genetic background of the Solanum lycopersicum cultivar M82. Fruit at the breaker and red ripe stages of ILs and BILs were harvested from the field at the Western Galilee Experimental Station in Akko, Israel. Samples represent methanol extracts analysed using a high-resolution UPLC/qTOF system comprised of a UPLC (Waters Acquity) which was connected online to a photodiode array (PDA) and qTOF detectors. Details on plant material and experimental protocols are provided in attached Methods file. Attached Metadata file provides all details on sample identity, measurement batches and quality controls.

Published
2020

29. Steroidal alkaloids defence metabolism and plant growth are modulated by the joint action of gibberellin and jasmonate signalling.

Author

Panda, Sayantan, Jozwiak, Adam, Sonawane, Prashant D., Szymanski, Jedrzej, Kazachkova, Yana, Vainer, Andrii, Vasuki Kilambi, Himabindu, Almekias‐Siegl, Efrat, Dikaya, Varvara, Bocobza, Samuel, Shohat, Hagai, Meir, Sagit, Wizler, Guy, Giri, Ashok P., Schuurink, Robert, Weiss, David, Yasuor, Hagai, Kamble, Avinash, and Aharoni, Asaph

Subjects
*GIBBERELLINS, *STEROIDAL alkaloids, *PLANT metabolism, *JASMONATE, *PLANT growth, *METABOLIC regulation
Abstract

Summary: Steroidal glycoalkaloids (SGAs) are protective metabolites constitutively produced by Solanaceae species. Genes and enzymes generating the vast structural diversity of SGAs have been largely identified. Yet, mechanisms of hormone pathways coordinating defence (jasmonate; JA) and growth (gibberellin; GA) controlling SGAs metabolism remain unclear.We used tomato to decipher the hormonal regulation of SGAs metabolism during growth vs defence tradeoff. This was performed by genetic and biochemical characterisation of different JA and GA pathways components, coupled with in vitro experiments to elucidate the crosstalk between these hormone pathways mediating SGAs metabolism.We discovered that reduced active JA results in decreased SGA production, while low levels of GA or its receptor led to elevated SGA accumulation. We showed that MYC1 and MYC2 transcription factors mediate the JA/GA crosstalk by transcriptional activation of SGA biosynthesis and GA catabolism genes. Furthermore, MYC1 and MYC2 transcriptionally regulate the GA signalling suppressor DELLA that by itself interferes in JA‐mediated SGA control by modulating MYC activity through protein–protein interaction. Chemical and fungal pathogen treatments reinforced the concept of JA/GA crosstalk during SGA metabolism.These findings revealed the mechanism of JA/GA interplay in SGA biosynthesis to balance the cost of chemical defence with growth. [ABSTRACT FROM AUTHOR]

Published
2022
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30. Auxin homeostasis in tomato and Arabidopsis under heat stress

Author

Breitenbach, Sarah, Panizel, Irina, Panda, Sayantan, Vainer, Andrii, Faigenboim, Adi, Aharoni, Asaph, Smolko, Ana, Salopek-Sondi, Branka, Bauer, Nataša, Yasour, Hagai, and Ludwig-Müller, Jutta

Subjects
auxin, tomato, Arabidopsis, heat stress, fungi, food and beverages
Abstract

The steady increase in temperature causes worldwide losses in agriculture, therefore heat stress is a problem in many areas in the world. Tomatoes are a major horticultural crop worldwide. Their yields are maximized in climates with moderate temperatures, whereas high temperature exposure limits tomato flower development, fruit set, and thus productivity. Experimental evidence indicates that reduced fruit set at high temperatures results from inhibited pollen development, anther release, and pollen viability reduction correlating with altered metabolism of the plant hormone auxin. We have therefore set out to analyze the auxin metabolome and transcriptome in tomato flower and fruit organs to identify candidates for alteration of auxin homeostasis. Among the strongly differentially regulated genes, four GH3 genes encoding auxin conjugate synthetases were specifically upregulated in male flower organs and gametophyte during flower development of tomato. We cloned these for heterologous expression in Escherichia coli to determine their in vitro activities. One highly regulated gene encoding an amino acid conjugate hydrolase has also been investigated in terms of activity. Since the generation of transgenic tomato plants is more time consuming than transformation of Arabidopsis, we have created transgenic lines overexpressing IAA amino acid conjugate hydrolases and GH3 genes from different sources and started to analyze these for possible heat stress tolerant phenotypes. Results from work with these transgenic plants will be presented.

Published
2018

31. The ‘TranSeq’ 3′‐end sequencing method for high‐throughput transcriptomics and gene space refinement in plant genomes

Author

Tzfadia, Oren, primary, Bocobza, Samuel, additional, Defoort, Jonas, additional, Almekias‐Siegl, Efrat, additional, Panda, Sayantan, additional, Levy, Matan, additional, Storme, Veronique, additional, Rombauts, Stephane, additional, Jaitin, Diego Adhemar, additional, Keren‐Shaul, Hadas, additional, Van de Peer, Yves, additional, and Aharoni, Asaph, additional

Published
2018
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32. Correction: Corrigendum: Plant cholesterol biosynthetic pathway overlaps with phytosterol metabolism

Author

Sonawane, Prashant D., primary, Pollier, Jacob, additional, Panda, Sayantan, additional, Szymanski, Jedrzej, additional, Massalha, Hassan, additional, Yona, Meital, additional, Unger, Tamar, additional, Malitsky, Sergey, additional, Arendt, Philipp, additional, Pauwels, Laurens, additional, Almekias-Siegl, Efrat, additional, Rogachev, Ilana, additional, Meir, Sagit, additional, Cárdenas, Pablo D., additional, Masri, Athar, additional, Petrikov, Marina, additional, Schaller, Hubert, additional, Schaffer, Arthur A., additional, Kamble, Avinash, additional, Giri, Ashok P., additional, Goossens, Alain, additional, and Aharoni, Asaph, additional

Published
2017
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33. Plant cholesterol biosynthetic pathway overlaps with phytosterol metabolism

Author

Sonawane, Prashant D., primary, Pollier, Jacob, additional, Panda, Sayantan, additional, Szymanski, Jedrzej, additional, Massalha, Hassan, additional, Yona, Meital, additional, Unger, Tamar, additional, Malitsky, Sergey, additional, Arendt, Philipp, additional, Pauwels, Laurens, additional, Almekias-Siegl, Efrat, additional, Rogachev, Ilana, additional, Meir, Sagit, additional, Cárdenas, Pablo D., additional, Masri, Athar, additional, Petrikov, Marina, additional, Schaller, Hubert, additional, Schaffer, Arthur A., additional, Kamble, Avinash, additional, Giri, Ashok P., additional, Goossens, Alain, additional, and Aharoni, Asaph, additional

Published
2016
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36. Plant cholesterol biosynthetic pathway overlaps with phytosterol metabolism

Author

Sonawane, Prashant D., Pollier, Jacob, Panda, Sayantan, Szymanski, Jedrzej, Massalha, Hassan, Yona, Meital, Unger, Tamar, Malitsky, Sergey, Arendt, Philipp, Pauwels, Laurens, Almekias-Siegl, Efrat, Rogachev, Ilana, Meir, Sagit, Cárdenas, Pablo D., Masri, Athar, Petrikov, Marina, Schaller, Hubert, Schaffer, Arthur A., Kamble, Avinash, Giri, Ashok P., Goossens, Alain, and Aharoni, Asaph

Abstract

The amount of cholesterol made by many plants is not negligible. Whereas cholesterogenesis in animals was elucidated decades ago, the plant pathway has remained enigmatic. Among other roles, cholesterol is a key precursor for thousands of bioactive plant metabolites, including the well-known Solanum steroidal glycoalkaloids. Integrating tomato transcript and protein co-expression data revealed candidate genes putatively associated with cholesterol biosynthesis. A combination of functional assays including gene silencing, examination of recombinant enzyme activity and yeast mutant complementation suggests the cholesterol pathway comprises 12 enzymes acting in 10 steps. It appears that half of the cholesterogenesis-specific enzymes evolved through gene duplication and divergence from phytosterol biosynthetic enzymes, whereas others act reciprocally in both cholesterol and phytosterol metabolism. Our findings provide a unique example of nature's capacity to exploit existing protein folds and catalytic machineries from primary metabolism to assemble a new, multi-step metabolic pathway. Finally, the engineering of a ‘high-cholesterol’ model plant underscores the future value of our gene toolbox to produce high-value steroidal compounds via synthetic biology.

Published
2017
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37. Corrigendum: Plant cholesterol biosynthetic pathway overlaps with phytosterol metabolism

Author

Sonawane, Prashant D., Pollier, Jacob, Panda, Sayantan, Szymanski, Jedrzej, Massalha, Hassan, Yona, Meital, Unger, Tamar, Malitsky, Sergey, Arendt, Philipp, Pauwels, Laurens, Almekias-Siegl, Efrat, Rogachev, Ilana, Meir, Sagit, Cárdenas, Pablo D., Masri, Athar, Petrikov, Marina, Schaller, Hubert, Schaffer, Arthur A., Kamble, Avinash, Giri, Ashok P., Goossens, Alain, and Aharoni, Asaph

Abstract

This corrects the article DOI: 10.1038/nplants.2016.205

Published
2017
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