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2. Thermopriming triggers splicing memory in Arabidopsis

Author

Ling, Yu, Serrano, Natalia, Gao, Ge, Atia, Mohamed, Mokhtar, Morad, Woo, Yong H., Bazin, Jeremie, Veluchamy, Alaguraj, Benhamed, Moussa, Crespi, Martin, Gehring, Christoph, Reddy, A.S.N., and Mahfouz, Magdy M.

Published
2018

5. The genome of Chenopodium quinoa

Author

Jarvis, David E., Ho, Yung Shwen, Lightfoot, Damien J., Schmckel, Sandra M., Li, Bo, Borm, Theo J. A., Ohyanagi, Hajime, Mineta, Katsuhiko, Michell, Craig T., Saber, Noha, Kharbatia, Najeh M., Rupper, Ryan R., Sharp, Aaron R., Dally, Nadine, Boughton, Berin A., Woo, Yong H., Gao, Ge, Schijlen, Elio G. W. M., Guo, Xiujie, Momin, Afaque A., Negro, Snia, Al-Babili, Salim, Gehring, Christoph, Roessner, Ute, Jung, Christian, Murphy, Kevin, Arold, Stefan T., Gojobori, Takashi, Linden, C. Gerard van der, van Loo, Eibertus N., Jellen, Eric N., Maughan, Peter J., and Tester, Mark

Subjects
DNA sequencing -- Methods, Quinoa -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa., Author(s): David E. Jarvis [1]; Yung Shwen Ho [1]; Damien J. Lightfoot [1]; Sandra M. Schmckel [1]; Bo Li [1]; Theo J. A. Borm [2]; Hajime Ohyanagi [3]; Katsuhiko Mineta [...]

Published
2017
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7. Corrigendum: The genome of Chenopodium quinoa

Author

Jarvis, David E., Ho, Yung Shwen, Lightfoot, Damien J., Schmckel, Sandra M., Li, Bo, Borm, Theo J. A., Ohyanagi, Hajime, Mineta, Katsuhiko, Michell, Craig T., Saber, Noha, Kharbatia, Najeh M., Rupper, Ryan R., Sharp, Aaron R., Dally, Nadine, Boughton, Berin A., Woo, Yong H., Gao, Ge, Schijlen, Elio G. W. M., Guo, Xiujie, Momin, Afaque A., Negro, Snia, Al-Babili, Salim, Gehring, Christoph, Roessner, Ute, Jung, Christian, Murphy, Kevin, Arold, Stefan T., Gojobori, Takashi, van der Linden, C. Gerard, van Loo, Eibertus N., Jellen, Eric N., Maughan, Peter J., and Tester, Mark

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): David E. Jarvis; Yung Shwen Ho; Damien J. Lightfoot; Sandra M. Schmckel; Bo Li; Theo J. A. Borm; Hajime Ohyanagi; Katsuhiko Mineta; Craig T. Michell; Noha Saber; Najeh M. [...]

Published
2017
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10. The genome of Chenopodium quinoa

Author

Jarvis, D.E., Shwen Ho, Yung, Lightfoot, Damien J., Schmöckel, Sandra M., Li, Bo, Borm, T.J.A., Ohyanagi, Hajime, Mineta, Katsuhiko, Mitchell, Craig T., Saber, Noha, Kharbatia, Najeh M., Rupper, Ryan R., Sharp, Aaron R., Dally, Nadine, Boughton, Berin A., Woo, Yong H., Gao, Ge, Schijlen, E.G.W.M., Guo, Xiujie, Momin, Afaque A., Negräo, Sónia, Al-Babili, Salim, Gehring, Christoph, Roessner, Ute, Jung, Christian, Murphy, Kevin, Arold, Stefan T., Gojobori, Takashi, van der Linden, C.G., van Loo, E.N., Jellen, Eric N., Maughan, Peter J., Tester, Mark, Jarvis, D.E., Shwen Ho, Yung, Lightfoot, Damien J., Schmöckel, Sandra M., Li, Bo, Borm, T.J.A., Ohyanagi, Hajime, Mineta, Katsuhiko, Mitchell, Craig T., Saber, Noha, Kharbatia, Najeh M., Rupper, Ryan R., Sharp, Aaron R., Dally, Nadine, Boughton, Berin A., Woo, Yong H., Gao, Ge, Schijlen, E.G.W.M., Guo, Xiujie, Momin, Afaque A., Negräo, Sónia, Al-Babili, Salim, Gehring, Christoph, Roessner, Ute, Jung, Christian, Murphy, Kevin, Arold, Stefan T., Gojobori, Takashi, van der Linden, C.G., van Loo, E.N., Jellen, Eric N., Maughan, Peter J., and Tester, Mark

Abstract

Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

Published
2017

11. Erratum: Corrigendum: The genome of Chenopodium quinoa

Author

Jarvis, David E., primary, Ho, Yung Shwen, additional, Lightfoot, Damien J., additional, Schmöckel, Sandra M., additional, Li, Bo, additional, Borm, Theo J. A., additional, Ohyanagi, Hajime, additional, Mineta, Katsuhiko, additional, Michell, Craig T., additional, Saber, Noha, additional, Kharbatia, Najeh M., additional, Rupper, Ryan R., additional, Sharp, Aaron R., additional, Dally, Nadine, additional, Boughton, Berin A., additional, Woo, Yong H., additional, Gao, Ge, additional, Schijlen, Elio G. W. M., additional, Guo, Xiujie, additional, Momin, Afaque A., additional, Negrão, Sónia, additional, Al-Babili, Salim, additional, Gehring, Christoph, additional, Roessner, Ute, additional, Jung, Christian, additional, Murphy, Kevin, additional, Arold, Stefan T., additional, Gojobori, Takashi, additional, van der Linden, C. Gerard, additional, van Loo, Eibertus N., additional, Jellen, Eric N., additional, Maughan, Peter J., additional, and Tester, Mark, additional

Published
2017
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12. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Author

Woo, Yong H, Ansari, Hifzur, Otto, Thomas D, Klinger, Christen M, Kolisko, Martin, Michalek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del, Campo Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G, Hajdušková, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J, Mast, Fred D, Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K, Rawlings, Neil D, Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E, Doerig, Christian, Bowler, Chris, Keeling, Patrick J, Roos, David S, Dacks, Joel B, Templeton, Thomas J, Waller, Ross F, Lukeš, Julius, Obornik, Miroslav, Pain, Arnab, Woo, Yong H, Ansari, Hifzur, Otto, Thomas D, Klinger, Christen M, Kolisko, Martin, Michalek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del, Campo Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G, Hajdušková, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J, Mast, Fred D, Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K, Rawlings, Neil D, Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E, Doerig, Christian, Bowler, Chris, Keeling, Patrick J, Roos, David S, Dacks, Joel B, Templeton, Thomas J, Waller, Ross F, Lukeš, Julius, Obornik, Miroslav, and Pain, Arnab

Abstract

The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga., eLife, 4, E06974; 2015

Published
2015

13. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Author

Woo, Yong H., Ansari, Hifzur, Otto, Thomas D., Klinger, Christen M., Kolisko, Martin, Michálek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del Campo, Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G., Hajduškova, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J., Mast, Fred D., Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K., Rawlings, Neil D., Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E., Doerig, Christian, Bowler, Chris, Keeling, Patrick J., Roos, David S., Dacks, Joel B., Templeton, Thomas J., Waller, Ross F., Lukeš, Julius, Oborník, Miroslav, Pain, Arnab, Woo, Yong H., Ansari, Hifzur, Otto, Thomas D., Klinger, Christen M., Kolisko, Martin, Michálek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del Campo, Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G., Hajduškova, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J., Mast, Fred D., Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K., Rawlings, Neil D., Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E., Doerig, Christian, Bowler, Chris, Keeling, Patrick J., Roos, David S., Dacks, Joel B., Templeton, Thomas J., Waller, Ross F., Lukeš, Julius, Oborník, Miroslav, and Pain, Arnab

Published
2015

14. Thermopriming triggers splicing memory in Arabidopsis.

Author

Yu Ling, Serrano, Natalia, Ge Gao, Atia, Mohamed, Mokhtar, Morad, Woo, Yong H., Bazin, Jeremie, Veluchamy, Alaguraj, Benhamed, Moussa, Crespi, Martin, Gehring, Christoph, Reddy, A. S. N., and Mahfouz, Magdy M.

Subjects
ABIOTIC stress, ENVIRONMENTAL sciences, AGRICULTURAL productivity, ARABIDOPSIS, PLANT genetics
Abstract

Abiotic and biotic stresses limit crop productivity. Exposure to a non-lethal stress, referred to as priming, can allow plants to survive subsequent and otherwise lethal conditions; the priming effect persists even after a prolonged stress-free period. However, the molecular mechanisms underlying priming are not fully understood. Here, we investigated the molecular basis of heat-shock memory and the role of priming in Arabidopsis thaliana. Comprehensive analysis of transcriptome-wide changes in gene expression and alternative splicing in primed and non-primed plants revealed that alternative splicing functions as a novel component of heat-shock memory. We show that priming of plants with a non-lethal heat stress results in de-repression of splicing after a second exposure to heat stress. By contrast, non-primed plants showed significant repression of splicing. These observations link 'splicing memory' to the ability of plants to survive subsequent and otherwise lethal heat stress. This newly discovered priming-induced splicing memory may represent a general feature of heat-stress responses in plants and other organisms as many of the key components are conserved among eukaryotes. Furthermore, this finding could facilitate the development of novel approaches to improve plant survival under extreme heat stress. [ABSTRACT FROM AUTHOR]

Published
2018
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15. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Author

Woo, Yong H, primary, Ansari, Hifzur, additional, Otto, Thomas D, additional, Klinger, Christen M, additional, Kolisko, Martin, additional, Michálek, Jan, additional, Saxena, Alka, additional, Shanmugam, Dhanasekaran, additional, Tayyrov, Annageldi, additional, Veluchamy, Alaguraj, additional, Ali, Shahjahan, additional, Bernal, Axel, additional, del Campo, Javier, additional, Cihlář, Jaromír, additional, Flegontov, Pavel, additional, Gornik, Sebastian G, additional, Hajdušková, Eva, additional, Horák, Aleš, additional, Janouškovec, Jan, additional, Katris, Nicholas J, additional, Mast, Fred D, additional, Miranda-Saavedra, Diego, additional, Mourier, Tobias, additional, Naeem, Raeece, additional, Nair, Mridul, additional, Panigrahi, Aswini K, additional, Rawlings, Neil D, additional, Padron-Regalado, Eriko, additional, Ramaprasad, Abhinay, additional, Samad, Nadira, additional, Tomčala, Aleš, additional, Wilkes, Jon, additional, Neafsey, Daniel E, additional, Doerig, Christian, additional, Bowler, Chris, additional, Keeling, Patrick J, additional, Roos, David S, additional, Dacks, Joel B, additional, Templeton, Thomas J, additional, Waller, Ross F, additional, Lukeš, Julius, additional, Oborník, Miroslav, additional, and Pain, Arnab, additional

Published
2015
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16. Author response: Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Author

Woo, Yong H, primary, Ansari, Hifzur, additional, Otto, Thomas D, additional, Klinger, Christen M, additional, Kolisko, Martin, additional, Michálek, Jan, additional, Saxena, Alka, additional, Shanmugam, Dhanasekaran, additional, Tayyrov, Annageldi, additional, Veluchamy, Alaguraj, additional, Ali, Shahjahan, additional, Bernal, Axel, additional, del Campo, Javier, additional, Cihlář, Jaromír, additional, Flegontov, Pavel, additional, Gornik, Sebastian G, additional, Hajdušková, Eva, additional, Horák, Aleš, additional, Janouškovec, Jan, additional, Katris, Nicholas J, additional, Mast, Fred D, additional, Miranda-Saavedra, Diego, additional, Mourier, Tobias, additional, Naeem, Raeece, additional, Nair, Mridul, additional, Panigrahi, Aswini K, additional, Rawlings, Neil D, additional, Padron-Regalado, Eriko, additional, Ramaprasad, Abhinay, additional, Samad, Nadira, additional, Tomčala, Aleš, additional, Wilkes, Jon, additional, Neafsey, Daniel E, additional, Doerig, Christian, additional, Bowler, Chris, additional, Keeling, Patrick J, additional, Roos, David S, additional, Dacks, Joel B, additional, Templeton, Thomas J, additional, Waller, Ross F, additional, Lukeš, Julius, additional, Oborník, Miroslav, additional, and Pain, Arnab, additional

Published
2015
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