Browsing by Author "Sederoff, Heike"

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    Amino Acids Are an Ineffective Fertilizer for Dunaliella spp. Growth
    Murphree, Colin A.; Dums, Jacob T.; Jain, Siddharth K.; Zhao, Chengsong; Young, Danielle Y.; Khoshnoodi, Nicole; Tikunov, Andrey; Macdonald, Jeffrey; Pilot, Guillaume; Sederoff, Heike (Frontiers, 2017-05-26)
    Autotrophic microalgae are a promising bioproducts platform. However, the fundamental requirements these organisms have for nitrogen fertilizer severely limit the impact and scale of their cultivation. As an alternative to inorganic fertilizers, we investigated the possibility of using amino acids from deconstructed biomass as a nitrogen source in the genus Dunaliella. We found that only four amino acids (glutamine, histidine, cysteine, and tryptophan) rescue Dunaliella spp. growth in nitrogen depleted media, and that supplementation of these amino acids altered the metabolic profile of Dunaliella cells. Our investigations revealed that histidine is transported across the cell membrane, and that glutamine and cysteine are not transported. Rather, glutamine, cysteine, and tryptophan are degraded in solution by a set of oxidative chemical reactions, releasing ammonium that in turn supports growth. Utilization of biomass-derived amino acids is therefore not a suitable option unless additional amino acid nitrogen uptake is enabled through genetic modifications of these algae.
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    One thousand plant transcriptomes and the phylogenomics of green plants
    Leebens-Mack, James H.; Barker, Michael S.; Carpenter, Eric J.; Deyholos, Michael K.; Gitzendanner, Matthew A.; Graham, Sean W.; Grosse, Ivo; Li, Zheng; Melkonian, Michael; Mirarab, Siavash; Porsch, Martin; Quint, Marcel; Rensing, Stefan A.; Soltis, Douglas E.; Soltis, Pamela S.; Stevenson, Dennis W.; Ullrich, Kristian K.; Wickett, Norman J.; DeGironimo, Lisa; Edger, Patrick P.; Jordon-Thaden, Ingrid E.; Joya, Steve; Liu, Tao; Melkonian, Barbara; Miles, Nicholas W.; Pokorny, Lisa; Quigley, Charlotte; Thomas, Philip; Villarreal, Juan Carlos; Augustin, Megan M.; Barrett, Matthew D.; Baucom, Regina S.; Beerling, David J.; Benstein, Ruben Maximilian; Biffin, Ed; Brockington, Samuel F.; Burge, Dylan O.; Burris, Jason N.; Burris, Kellie P.; Burtet-Sarramegna, Valerie; Caicedo, Ana L.; Cannon, Steven B.; Cebi, Zehra; Chang, Ying; Chater, Caspar; Cheeseman, John M.; Chen, Tao; Clarke, Neil D.; Clayton, Harmony; Covshoff, Sarah; Crandall-Stotler, Barbara J.; Cross, Hugh; dePamphilis, Claude W.; Der, Joshua P.; Determann, Ron; Dickson, Rowan C.; Di Stilio, Veronica S.; Ellis, Shona; Fast, Eva; Feja, Nicole; Field, Katie J.; Filatov, Dmitry A.; Finnegan, Patrick M.; Floyd, Sandra K.; Fogliani, Bruno; Garcia, Nicolas; Gateble, Gildas; Godden, Grant T.; Goh, Falicia (Qi Yun); Greiner, Stephan; Harkess, Alex; Heaney, James Mike; Helliwell, Katherine E.; Heyduk, Karolina; Hibberd, Julian M.; Hodel, Richard G. J.; Hollingsworth, Peter M.; Johnson, Marc T. J.; Jost, Ricarda; Joyce, Blake; Kapralov, Maxim V.; Kazamia, Elena; Kellogg, Elizabeth A.; Koch, Marcus A.; Von Konrat, Matt; Konyves, Kalman; Kutchan, Toni M.; Lam, Vivienne; Larsson, Anders; Leitch, Andrew R.; Lentz, Roswitha; Li, Fay-Wei; Lowe, Andrew J.; Ludwig, Martha; Manos, Paul S.; Mavrodiev, Evgeny; McCormick, Melissa K.; McKain, Michael; McLellan, Tracy; McNeal, Joel R.; Miller, Richard E.; Nelson, Matthew N.; Peng, Yanhui; Ralph, Paula E.; Real, Daniel; Riggins, Chance W.; Ruhsam, Markus; Sage, Rowan F.; Sakai, Ann K.; Scascitella, Moira; Schilling, Edward E.; Schlosser, Eva-Marie; Sederoff, Heike; Servick, Stein; Sessa, Emily B.; Shaw, A. Jonathan; Shaw, Shane W.; Sigel, Erin M.; Skema, Cynthia; Smith, Alison G.; Smithson, Ann; Stewart, C. Neal, Jr.; Stinchcombe, John R.; Szovenyi, Peter; Tate, Jennifer A.; Tiebel, Helga; Trapnell, Dorset; Villegente, Matthieu; Wang, Chun-Neng; Weller, Stephen G.; Wenzel, Michael; Weststrand, Stina; Westwood, James H.; Whigham, Dennis F.; Wu, Shuangxiu; Wulff, Adrien S.; Yang, Yu; Zhu, Dan; Zhuang, Cuili; Zuidof, Jennifer; Chase, Mark W.; Pires, J. Chris; Rothfels, Carl J.; Yu, Jun; Chen, Cui; Chen, Li; Cheng, Shifeng; Li, Juanjuan; Li, Ran; Li, Xia; Lu, Haorong; Ou, Yanxiang; Sun, Xiao; Tan, Xuemei; Tang, Jingbo; Tian, Zhijian; Wang, Feng; Wang, Jun; Wei, Xiaofeng; Xu, Xun; Yan, Zhixiang; Yang, Fan; Zhong, Xiaoni; Zhou, Feiyu; Zhu, Ying; Zhang, Yong; Ayyampalayam, Saravanaraj; Barkman, Todd J.; Nam-Phuong Nguyen; Matasci, Naim; Nelson, David R.; Sayyari, Erfan; Wafula, Eric K.; Walls, Ramona L.; Warnow, Tandy; An, Hong; Arrigo, Nils; Baniaga, Anthony E.; Galuska, Sally; Jorgensen, Stacy A.; Kidder, Thomas I.; Kong, Hanghui; Lu-Irving, Patricia; Marx, Hannah E.; Qi, Xinshuai; Reardon, Chris R.; Sutherland, Brittany L.; Tiley, George P.; Welles, Shana R.; Yu, Rongpei; Zhan, Shing; Gramzow, Lydia; Theissen, Gunter; Wong, Gane Ka-Shu (2019-10-31)
    Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.