RNA-seq analysis and transcriptome assembly of Salicornia neei reveals a powerful system for ammonium detoxification

Electronic Journal of Biotechnology - Tập 58 - Trang 70-81 - 2022
Mónica Díaz-Silva1, Jonathan Maldonado2,3, Pamela Veloso1, Nicol Delgado1, Herman Silva2, José A. Gallardo1
1Laboratorio de Genética y Genómica Aplicada, Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
2Laboratorio de Genómica Funcional & Bioinformática, Facultad de Ciencias Agronómicas, Universidad de Chile, Av. Santa Rosa 11315, 8820808 La Pintana, Santiago, Chile
3Laboratorio de Multiómica Vegetal y Bioinformática, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile

Tài liệu tham khảo

Diaz, 2020, Efficiency of Salicornia neei to treat aquaculture effluent from a hypersaline and artificial wetland, Agriculture, 10, 621, 10.3390/agriculture10120621 Alonso, 2008, Taxonomic and nomenclatural notes on South American taxa of Sarcocornia (Chenopodiaceae), Ann Bot Fenn, 45, 241, 10.5735/085.045.0401 Riquelme, 2016, Nutritional and functional characterization of wild and cultivated Sarcocornia neei grown in Chile, Cienc Inv Agr, 43, 283, 10.4067/S0718-16202016000200011 Alonso, 2010, Effect of salinity on the germination of Sarcocornia neei (Chenopodiaceae) from two contrasting habitats, Seed Sci Technol, 45, 252, 10.15258/sst.2017.45.1.20 Beyer, 2021, Sarcocornia neei: A novel halophyte species for bioremediation of marine aquaculture wastewater and production diversification in integrated systems, Aquaculture, 543, 737961, 10.1016/j.aquaculture.2021.736971 de Souza, 2018, Growth, phenolics, photosynthetic pigments, and antioxidant response of two new genotypes of sea asparagus (Salicornia neei Lag.) to salinity under greenhouse and field conditions, Agriculture, 8, 115, 10.3390/agriculture8070115 Quinta, 2015, Growth and nitrogen uptake by Salicornia europaea and Aster tripolium in nutrient conditions typical of aquaculture wastewater, Chemosphere, 120, 414, 10.1016/j.chemosphere.2014.08.017 Turcios, 2014, Sustainable treatment of aquaculture effluents-what can we learn from the past for the future?, Sustainability, 6, 836, 10.3390/su6020836 Islam, 2015, Nitrogen and phosphorus budget in coastal and marine cage aquaculture and impacts of effluent loading on ecosystem: review and analysis towards model development, Mar Pollut Bull, 50, 48, 10.1016/j.marpolbul.2004.08.008 Maillard, 2005, Water quality and sludge characterization at raceway-system trout farms, Aquacult Eng, 33, 271, 10.1016/j.aquaeng.2005.02.006 Bisogni, 1994, Control of pH in closed cycle aquaculture systems, Dev Aquacult Fish Sci, 27, 235 Bower, 1978, Ionization of ammonia in seawater: effects of temperature, pH, and salinity, J Fish Res Board Can, 35, 1012, 10.1139/f78-165 Carballeira, 2012, Implementation of a minimal set of biological tests to assess the ecotoxic effects of effluents from land-based marine fish farms, Ecotoxicol Environ Saf, 78, 148, 10.1016/j.ecoenv.2011.11.022 Playchoom C, Pungrasmi W, Powtongsook S. Effect of carbon sources and carbon/nitrogen ratio on nitrate removal in aquaculture denitrification tank. International conference on biology, environment and chemistry, Singapore 2011;1:307-311. Shpigel, 2013, Constructed wetland with Salicornia as a biofilter for mariculture effluents, Aquaculture, 412–413, 52, 10.1016/j.aquaculture.2013.06.038 Brown, 1999, Halophytes for the treatment of saline aquaculture effluent, Aquaculture, 175, 255, 10.1016/S0044-8486(99)00084-8 Cao, 2007, Environmental impact of aquaculture and countermeasures to aquaculture pollution in China, Environ Sci Pollut Res, 14, 452, 10.1065/espr2007.05.426 Cloern, 2001, Our evolving conceptual model of the coastal eutrophication problem, Mar Ecol Prog, 210, 223, 10.3354/meps210223 Holmer, 2005, Organic enrichment from marine finfish aquaculture and effects on sediment biogeochemical processes, 181 Hu, 2015, Effect of plant species on nitrogen recovery in aquaponics, Bioresour Technol, 188, 92, 10.1016/j.biortech.2015.01.013 Meade, 1985, Allowable ammonia for fish culture, Prog Fish-Cult, 47, 135, 10.1577/1548-8640(1985)47<135:AAFFC>2.0.CO;2 Waller, 2015, Integrated multi-trophic aquaculture in a zero-exchange recirculation aquaculture system for marine fish and hydroponic halophyte production, Aquacult Int, 23, 1473, 10.1007/s10499-015-9898-3 Ravazzolo, 2020, Nitrate and ammonium affect the overall maize response to nitrogen availability by triggering specific and common transcriptional signatures in roots, Int J Mol Sci, 21, 686, 10.3390/ijms21020686 Coleto, 2021, Arabidopsis thaliana transcription factors MYB28 and MYB29 shape ammonium stress responses by regulating Fe homeostasis, New Phytol, 229, 1021, 10.1111/nph.16918 Britto, 2002, NH4+ toxicity in higher plants: a critical review, J Plant Physiol, 159, 567, 10.1078/0176-1617-0774 Tang, 2011, The combined effects of salinity and nitrogen forms on Catharanthus roseus: The role of internal ammonium and free amino acids during salt stress, J Soil Sci Plant, 174, 135, 10.1002/jpln.200900354 Cruz, 2006, How does glutamine synthetase activity determine plant tolerance to ammonium?, Planta, 223, 1068, 10.1007/s00425-005-0155-2 Liu, 2017, Ammonium as a signal for physiological and morphological responses in plants, J Exp Bot, 68, 2581, 10.1093/jxb/erx086 Meng, 2018, Mechanisms of salt tolerance in halophytes: current understanding and recent advances, Open Life Sci, 13, 149, 10.1515/biol-2018-0020 Ma, 2020, Regulation of ammonium cellular levels is an important adaptive trait for the euhalophytic behavior of Salicornia europaea, Plants, 9, 257, 10.3390/plants9020257 Ashraf, 2018, Salinity effects on nitrogen metabolism in plants - focusing on the activities of nitrogen metabolizing enzymes: A review, J Plant Nutr, 41, 1065, 10.1080/01904167.2018.1431670 Stewart, 1978, Nitrogen-metabolism of halophytes III. Enzymes of ammonia assimilation, New Phytol, 80, 307, 10.1111/j.1469-8137.1978.tb01563.x Gutiérrez, 2008, Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1, PNAS, 105, 4939, 10.1073/pnas.0800211105 Yokoishi, 1994, Seed-germination of the halophyte Suaeda japonica under salt stress, J Plant Res, 107, 385, 10.1007/BF02344061 Kumari, 2015, Proteomics, metabolomics, and ionomics perspectives of salinity tolerance in halophytes, Front Plant Sci, 6, 537, 10.3389/fpls.2015.00537 Crosby, 1968, Determination of ammonia by the Nessler method in waters containing hydrazine, Analyst, 93, 406, 10.1039/an9689300406 Adamowicz, 1999, Trends in modelling nitrate uptake, Acta Horticult, 507, 231, 10.17660/ActaHortic.1999.507.27 Chang, 1993, A simple and efficient method for isolating RNA from pine trees, Plant Mol Biol Report, 11, 113, 10.1007/BF02670468 Lal, 2001, RNA isolation from high phenolic tea leaves and buds, Plant Mol Biol Report, 19, 181, 10.1007/BF02772161 Meisel, 2005, A rapid and efficient method for purifying high quality total RNA from peaches (Prunus persica) for functional genomics analyses, Biol Res, 38, 83, 10.4067/S0716-97602005000100010 Camacho, 2009, BLAST+: architecture and applications, BMC Bioinf, 10, 421, 10.1186/1471-2105-10-421 Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610 Kal, 1999, Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources, Mol Biol Cell, 10, 1859, 10.1091/mbc.10.6.1859 Bolstad, 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19, 185, 10.1093/bioinformatics/19.2.185 Morales A, Zurita-Silva A, Maldonado J, et al. Transcriptional responses of chilean quinoa (Chenopodium quinoa Willd.) under water deficit conditions uncovers ABA-independent expression patterns. Front Plant Sci 2017;8:216. https://doi.org/10.3389/fpls.2017.00216 PMid: 28337209. Ramos-Ruiz, 2018, GABA, a non-protein amino acid ubiquitous in food matrices, Cogent Food Agric, 4, 1534323, 10.1080/23311932.2018.1534323 Hu, 2017, Effect of salinity on the performance of constructed wetlands treating mariculture wastewater with different halophytes and its molecular biological mechanism, Desalin Water Treat, 99, 255, 10.5004/dwt.2017.21702 Wang, 2019, Association of transcription factor WRKY56 gene from Populus simonii x P. nigra with salt tolerance in Arabidopsis thaliana, PeerJ, 7, e7291, 10.7717/peerj.7291 Le Gall, 2015, Cell wall metabolism in response to abiotic stress, Plants, 4, 112, 10.3390/plants4010112 Kesten, 2017, Regulation of cellulose synthesis in response to stress, Curr Opin in Plant Biol, 40, 106, 10.1016/j.pbi.2017.08.010 Tenhaken, 2015, Cell wall remodeling under abiotic stress, Front Plant Sci, 5, 771, 10.3389/fpls.2014.00771 Walia, 2005, Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage, Plant Physiol, 139, 822, 10.1104/pp.105.065961 Wang, 2020, Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum, BMC Genomics, 21, 838, 10.1186/s12864-020-07260-z Jiao, 2021, Short-term transcriptomic responses of Populus euphratica roots and leaves to drought stress, J For Res, 32, 841, 10.1007/s11676-020-01123-9 Li, 2014, Characterization of soybean beta-expansin genes and their expression responses to symbiosis, nutrient deficiency, and hormone treatment, Appl Microbiol Biotechnol, 98, 2805, 10.1007/s00253-013-5240-z Sun L, Di DW, Li GJ, et al. Spatio-temporal dynamics in global rice gene expression (Oryza sativa L.) in response to high ammonium stress. J Plant Physiol 2017;212:94-104. https://doi.org/10.1016/j.jplph.2017.02.006 PMid: 28282528. Jan, 2021, Plant secondary metabolite biosynthesis and transcriptional regulation in response to biotic and abiotic stress conditions, Agronomy, 11, 968, 10.3390/agronomy11050968 Zhao, 2021, Transcriptome analysis revealed plant hormone biosynthesis and response pathway modification by Epichloe gansuensis in Achnatherum inebrians under different soil moisture availability, J Fungi, 7, 640, 10.3390/jof7080640 Binder, 2020, Ethylene signaling in plants, J Biol Chem, 295, 7710, 10.1074/jbc.REV120.010854 '] Chen K, Li GJ, Bressan RA, et al. Abscisic acid dynamics, signaling, and functions in plants. J Integr Plant Biol 2020;62(1):25-54. https://doi.org/10.1111/jipb.12899 PMid: 31850654. Ellouzi, 2014, A comparative study of the early osmotic, ionic, redox and hormonal signaling response in leaves and roots of two halophytes and a glycophyte to salinity, Planta, 240, 1299, 10.1007/s00425-014-2154-7 Verma V, Ravindran P, Kumar PP. Plant hormone-mediated regulation of stress responses. BMC Plant Biol 2016;6:86. https://doi.org/10.1186/s12870-016-0771-y PMid: 27079791. Li, 2011, The ethylene response factor AtERF11 that is transcriptionally modulated by the bZIP transcription factor HY5 is a crucial repressor for ethylene biosynthesis in Arabidopsis, Plant J, 68, 88, 10.1111/j.1365-313X.2011.04670.x Madhavan, 1983, Effect of ethylene on stomatal opening in tomato and carnation leaves, Plant Cell Physiol, 24, 569 Polko, 2019, 1-Aminocyclopropane 1-carboxylic acid and its emerging role as an ethylene-independent growth regulator, Front Plant Sci, 10, 1602, 10.3389/fpls.2019.01602 Zapata, 2017, Short term effect of salt shock on ethylene and polyamines depends on plant salt sensitivity, Front Plant Sci, 8, 855, 10.3389/fpls.2017.00855 Pandey, 2000, Role of polyamines and ethylene as modulators of plant senescence, J Biosci, 25, 291, 10.1007/BF02703938 Gupta, 2013, Plant polyamines in abiotic stress responses, Acta Physiol Plant, 35, 2015, 10.1007/s11738-013-1239-4 Kumar N, Mallick S. Ameliorative Mechanisms of polyamines against abiotic stress in the rice plants. In: Hasanuzzaman M, Fujita M, Nahar K, et al. (eds) Advances in rice research for abiotic stress tolerance, Woodhead Publishing, 2019;35:725-735. https://doi.org/10.1016/B978-0-12-814332-2.00035-6 PMCid: PMC6678468. Bouchereau, 1999, Polyamines and environmental challenges: recent development, Plant Sci, 140, 103, 10.1016/S0168-9452(98)00218-0 Liu, 2016, Response of polyamine pools in marine phytoplankton to nutrient limitation and variation in temperature and salinity, Mar Ecol Prog Ser, 544, 93, 10.3354/meps11583 Tavladoraki, 2006, Heterologous expression and biochemical characterization of a polyamine oxidase from Arabidopsis involved in polyamine back conversion, Plant Physiol, 141, 1519, 10.1104/pp.106.080911 Moschou, 2008, Plant polyamine catabolism: The state of the art, Plant Signal Behav, 3, 1061, 10.4161/psb.3.12.7172 Flowers, 2015, Plant salt tolerance: adaptations in halophytes, Annals Bot, 115, 327, 10.1093/aob/mcu267 Thursby, 1984, Interaction of leaves and roots of Ruppia maritima in the uptake of phosphate, ammonia and nitrate, Mar Biol, 83, 61, 10.1007/BF00393086 Liu, 2009, Autophagy is required for tolerance of drought and salt stress in plants, Autophagy, 5, 954, 10.4161/auto.5.7.9290 Signorelli S, Tarkowski LP, Van den Ende, et al. Linking autophagy to abiotic and biotic stress responses. Trends Plant Sci 2019;24(5);413-430. https://doi.org/10.1016/j.tplants.2019.02.001 PMid: 30824355. Howitt, 2000, Structure, function and regulation of ammonium transporters in plants, Biochim Biophys Acta Biomembr, 1465, 152, 10.1016/S0005-2736(00)00136-X Martinoia, 2007, Vacuolar transporters and their essential role in plant metabolism, J Exp Bot, 58, 83, 10.1093/jxb/erl183 Chen, 2019, Autophagy and nutrients management in plants, Cells, 8, 1426, 10.3390/cells8111426 Luo, 2017, Autophagy is rapidly induced by salt stress and is required for salt tolerance in Arabidopsis, Front Plant Sci, 8, 1559, 10.3389/fpls.2017.01459 He, 2007, Atg9 trafficking in autophagy-related pathways, Autophagy, 3, 271, 10.4161/auto.3912 Johansen, 2011, Selective autophagy mediated by autophagic adapter proteins, Autophagy, 7, 279, 10.4161/auto.7.3.14487 Marino, 2019, Can ammonium stress be positive for plant performance?, Front Plant Sci, 10, 1103, 10.3389/fpls.2019.01103 Patterson, 2010, Distinct signalling pathways and transcriptome response signatures differentiate ammonium- and nitrate-supplied plants, Plant Cell Environ, 33, 1486 Yao, 2011, Kinetics of ammonium, nitrate and phosphate uptake by candidate plants used in constructed wetlands, Procedia Environ Sci, 10, 1854, 10.1016/j.proenv.2011.09.290