Here are the publications that the Department of Plant Sciences has produced since we started keeping a record in late 2015. It is probably not a complete list:
2019
Bussell EH, Dangerfield CE, Gilligan CA, Cunniffe NJ. (2019) Applying optimal control theory to complex epidemiological models to inform real-world disease management. The Royal Society https://doi.org/10.1098/rstb.2018.0284
Adnan S, Maltamo M, Coomes DA, Garcia-Abril A, Malhi Y, Manzanera JA, Butt N, Morecroft M, Valbuena R. (2019) A simple approach to forest structure classification using airborne laser scanning that can be adopted across bioregions. Forest Ecology and Management https://doi.org/10.1016/j.foreco.2018.10.057
Lambing C, Tock AJ, Choi K, Topp SD, Kuo PC, Blackwell AR, Zhao X, Osman K, Higgins JD, Franklin FCH, Henderson IR. (2019) REC8-cohesin, chromatin and transcription orchestrate meiotic recombination in the Arabidopsis genome. bioRxiv https://doi.org/10.1101/512400
Navarro FJ, Baulcombe DC. (2019) miRNA-mediated regulation of synthetic gene circuits in the green alga Chlamydomonas reinhardtii. ACS Synth. Biol. https://dx.doi.org/10.1021/acssynbio.8b00393
Horwath AB, Royles J, Tito R, Gudiño JA, Allen NS, Farfan-Rios W, Rapp JM, Silman MR, Malhi Y, Swamy V, Latorre Farfan JP, Griffiths H. (2019) Bryophyte stable isotope composition, diversity and biomass define tropical montane cloud forest extent. Proceedings of the Royal Society B:Biological Sciences https://doi.org/10.1098/rspb.2018.2284
Zellweger F, De Frenne P, Lenoir J, Rocchini D, Coomes DA. (2019) Advances in Microclimate Ecology Arising from Remote Sensing. Trends in Ecology and Evolution https://doi.org/10.1016/j.tree.2018.12.012
Matthus E, Wilkins KA, Swarbreck SM, Doddrell NH, Doccula FG, Costa A, Davies JM. (2019) Phosphate starvation alters abiotic stress-induced cytosolic free calcium increases in roots. Plant Physiology https://doi.org/10.1104/pp.18.01469
Kirkbride RC, Lu J, Zhang C, Mosher RA, Baulcombe DC, Chen ZJ. (2019) Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in Arabidopsis. PNAS https://doi.org/10.1073/pnas.1807621116
Swarbreck SM, Guerringue Y, Matthus E, Jamieson FJC, Davies JM. (2019) Impairment in karrikin but not strigolactone sensing enhances root skewing in Arabidopsis thaliana. The Plant Journal https://doi.org/10.1111/tpj.14233
Webb AAR, Seki M, Satake A, Caldana C. (2019) Continuous dynamic adjustment of the plant circadian oscillator. Nature Communications https://doi.org/10.1038/s41467-019-08398-5
Igea J, Tanentzap AJ. (2019) Multiple macroevolutionary routes to becoming a biodiversity hotspot. Science Advances https://doi.org/10.1126/sciadv.aau8067
Watkinson-Powell B, Gilligan CA, Cunniffe NJ. (2019) When does spatial diversification usefully maximise the durability of crop disease resistance?. bioRxiv https://doi.org/10.1101/540013
Mombaerts L, Carignano A, Robertson FR, Hearn TJ, Junyan J, Hayden D, Rutterford Z, Hotta CT, Hubbard KE, Mart Ruiz CM, Yuan Ye, Hannah MA, Goncalves J, Webb AAR. (2019) Dynamical differential expression (DyDE) . PLOS Computational Biology https://doi.org/10.1371/journal.pcbi.1006674
Roth R, Hillmer S, Funaya C, Chiapello M, Schumacher K, Lo Presti L, Kahmann R, Paszkowski U. (2019) Arbuscular cell invasion coincides with extracellular vesicles and membrane tubules. Nature Plants https://doi.org/10.1038/s41477-019-0365-4
Symington HA, Glover BJ. (2019) SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy. Plant Methods https://doi.org/10.1186/s13007-019-0403-2
Davey MP, Norman L, Sterk P, Huete-Ortega M, Bunbury F, Kin Wai Loh B, Stockton S, Peck LS, Convey P, Newsham KK, Smith AG. (2019) Snow algae communities in Antarctica: metabolic and taxonomic composition. New Phytologist http://dx.doi.org/10.1111/nph.15701
Worrall EA, Bravo-Cazar A, Nilon AT, Fletcher SJ, Robinson KE, Carr JP, Mitter N. (2019) Exogenous Application of RNAi-Inducing Double-Stranded RNA Inhibits Aphid-Mediated Transmission of a Plant Virus. Frontiers in Plant Science https://doi.org/10.3389/fpls.2019.00265
van Rongen M, Bennett T, Ticchiarelli F, Leyser O. (2019) Connective auxin transport contributes to strigolactone-mediated shoot branching control independent of the transcription factor BRC1. PLOS Genetics https://doi.org/10.1371/journal.pgen.1008023
Gorchs Rovira A, Smith AG. (2019) PPR proteins – orchestrators of organelle RNA metabolism. Physiologia Plantarum https://doi.org/10.1111/ppl.12950
Schreier TB, Hibberd JM. (2019) Variations in the Calvin–Benson cycle: selection pressures and optimization?. Journal of Experimental Botany https://doi.org/10.1093/jxb/erz078
Swinfield T, Lindsell JA, Williams JV, Harrison RD, Agustiono, Habibi, Gemita E, Schönlieb CB, Coomes DA. (2019) Accurate Measurement of Tropical Forest Canopy Heights and Aboveground Carbon Using Structure From Motion. Remote Sensing https://doi.org/10.3390/rs11080928
Donnelly R, Cunniffe NJ, Carr JP, Gilligan CA. (2019) Pathogenic modification of plants enhances long‐distance dispersal of non‐persistently transmitted viruses to new hosts. Ecological Society of America https://doi.org/10.1002/ecy.2725
Giuliani R, Karki S, Covshoff S, Lin H-C, Coe RA, Koteyeva NC, WP Quick, Von Caemmerer S, Furbank RT, Hibberd JM, Edwards GE, Cousins AB. (2019) Knockdown of glycine decarboxylase complex alters photorespiratory carbon isotope fractionation in Oryza sativa leaves. Journal of Experimental Botany https://doi.org/10.1093/jxb/erz083
Hamelin FM, Allen LJS, Bokil VA, Gross LJ, Hilker FM, Jeger MJ, Manore CA, Power AG, Rúa MA, Cunniffe NJ. (2019) Co-infections by non-interacting pathogens are not independent & require new tests of interaction. bioRxiv https://doi.org/10.1101/618900
Buayam N, Davey MP, Smith AG, Pumas C. (2019) Effects of Copper and pH on the Growth and Physiology of Desmodesmus sp. AARLG074. Metabolites https://doi.org/10.3390/metabo9050084
Igea J, Tanentzap AJ. (2019) Angiosperm speciation speeds up near the poles. bioRxiv https://doi.org/10.1101/619064
Aubr-Kientz M, Dutrieux R, Ferrax A, Saatchi S, Hamraz H, Williams J, Coomes D, Piboule A, Vincent G. (2019) A Comparative Assessment of the Performance of Individual Tree Crowns Delineation Algorithms from ALS Data in Tropical Forests. Remote Sensing https://doi.org/10.3390/rs11091086
Hua L, Hibberd JM. (2019) An optimised protocol for isolation of RNA through laser capture microdissection of leaf material. bioRxiv https://doi.org/10.1101/644997
Giolio C, Moyroud E, Glover BJ, Kalberer M. (2019) Direct depolymerization coupled to liquid extraction surface analysis high-resolution mass spectrometry for the characterization of the surface of plant tissues. Analytical Chemistry https://doi.org/10.1021/acs.analchem.9b01094
Luginbuehl LH, El-Sharnouby S, Wang N, Hibberd JM. (2019) Fluorescent reporters for functional analysis in rice leaves. bioRxiv https://doi.org/10.1101/649160
Büntgen U, Krusic PJ, Piermattei A, Coomes DA, Esper J, Myglan VS, Kirdyanov AV, Camarero J, Crivallero A, Körner C. (2019) Limited capacity of tree growth to mitigate the global greenhouse effect under predicted warming.. Nat Commun https://doi.org/10.1038/s41467-019-10174-4
Steidinger BS, Crowther TW, Liang J, Van Nuland ME, Werner GDA, Reich PB, Nabuurs G, de-Miguel S, Zhou M, Picard N, Herault B, Zhao X, Zhang C, Routh D, Peay KG, GFBI consortium (2019) Climatic controls of decomposition drive the global biogeography of forest-tree symbioses.. Nature https://doi.org/10.1038/s41586-019-1128-0
Liu J, Slik F, Coomes D, Corlett RT, Wang Y, Wilson M, Hu G, Ding P, Yu M. (2019) The distribution of plants and seed dispersers in response to habitat fragmentation in an artificial island archipelago.. Journal of Biogeography https://doi.org/10.1111/jbi.13568
Liu J, Coomes DA, Gibson L, Hu G, Liu J, Luo Y, Wu C, Yu M. (2019) Forest fragmentation in China and its effect on biodiversity.. Biol Rev Camb Philos Soc. https://doi.org/10.1111/brv.12519
Spriggs RA, Vanderwel MC, Jones TA, Caspersen JP, Coomes DA. (2019) A critique of general allometry-inspired models for estimating forest carbon density from airborne LiDAR.. PLoS One https://doi.org/10.1371/journal.pone.0215238
Burgess SJ, Reyna-Llorens I, Stevenson SR, Singh P, Jaeger K, Hibberd JM. (2019) Genome-wide transcription factor binding in leaves from C3 and C4 grasses. bioRxiv https://doi.org/10.1101/165787
Baulcombe DC. (2019) How Virus Resistance Provided a Mechanistic Foundation for RNA Silencing. Plant Cell https://doi.org/10.1105/tpc.19.00348
Chiu CH, Paszkowski U. (2019) Mechanisms and Impact of Symbiotic Phosphate Acquisition. Cold Spring Harbor Perspectives in Biology https://doi.org/10.1101/cshperspect.a034603
Aguilar-Cruz A, Grimanelli D, Haseloff J, Arteaga-Vázquez MA. (2019) DNA methylation in Marchantia polymorpha. New Phytologist https://doi.org/10.1111/nph.15818
Nunes MH, Both S, Bongalov B, Brelsford C, Khoury S, Burslem D, Philipson C, Majalap N, Riutta T, Coomes D, Cutler M. (2019) Changes in leaf functional traits of rainforest canopy trees associated with an El Niño event in Borneo. Environmental Research Letters https://doi.org/10.1088/1748-9326/ab2eae
Swarbreck SM, Wang M, Wang Y, Kindred D, Sylvester-Bradley R, Shi W, Varinderpal-Sing, Bentley AR, Griffiths H. (2019) A Roadmap for Lowering Crop Nitrogen Requirement. Trends in Plant Science https://doi.org/10.1016/j.tplants.2019.06.006
Tmoneda A, Feng T, Sheehan H, Walker-Hale N, Pucker B, Lopez-Nieves S, Guo R, Brockington S. (2019) The evolution of betalain biosynthesis in Caryophyllales. New Phytologist https://doi.org/10.1111/nph.15980
Reynolds SA, Davey MP, Aldridge DC. (2019) Harnessing Synthetic Ecology for commercial algae production. Scientific Reports https://doi.org/10.1038/s41598-019-46135-6
Bongalov B, Burslem DFRP, Jucker T, Thompson SED, Rosindell J, Swinfield T, Nilus R, Clewley D, Phillips OL, Coomes DA. (2019) Reconciling the contribution of environmental and stochastic structuring of tropical forest diversity through the lens of imaging spectroscopy. Ecology Letters https://doi.org/10.1111/ele.13357
Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. (2019) Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis. Current Biology https://doi.org/10.1016/j.cub.2019.06.084
Gorgens EB, Motta A Z, Assis M, Nunes M, Jackson T, Coomes D, Rosette J, Oliveira e Cris Aragão LE, Ometto JP. (2019) The giant trees of the Amazon basin. Frontiers in the Ecology and Environment https://doi.org/10.1002/fee.2085
Yuan W, Jian T, Du K, Chen H, Cao Y, Xie J, Li M, Carr JP, Wu B, Fan Z, Zhou T. (2019) Maize phenylalanine ammonia‐lyases contribute to resistance to Sugarcane mosaic virus infection, most likely through positive regulation of salicylic acid accumulation. Molecular Plant Pathology https://doi.org/10.1111/mpp.12817
Hua L, Hibberd JM. (2019) An optimized protocol for isolation of high‐quality RNA through laser capture microdissection of leaf material. Plant Direct https://doi.org/10.1002/pld3.156
Burgess SJ, Reyna-Llorens I, Stevenson SR, Singh P, Jaeger K, Hibberd JM. (2019) Genome-wide transcription factor binding in leaves from C3 and C4 grasses. The Plant Cell https://doi.org/10.1105/tpc.19.00078
Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. (2019) Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis. Current Biology https://doi.org/10.1016/j.cub.2019.06.084
Benoit M, Drost H-G, Catoni M, Gouil Q, Lopez-Gomollon S, Baulcombe D, Paszkowski J. (2019) Environmental and epigenetic regulation of Rider retrotransposons in tomato. PLOS Genetics https://doi.org/10.1371/journal.pgen.1008370
Wang L, Stacey G, Leblanc-Fournier N, Legué V, Moulia B, Davies JM. (2019) Early Extracellular ATP Signaling in Arabidopsis Root Epidermis: A Multi-Conductance Process. Frontiers in Plant Science https://doi.org/10.3389/fpls.2019.01064
Thompson RN, Gilligan CA, Cunniffe NJ. (2019) When does a minor outbreak become a major epidemic? Linking the risk from invading pathogens to practical definitions of a major epidemic. bioRxiv https://doi.org/10.1101/768853
Bussell EH, Cunniffe NJ. (2019) Ongoing surveillance protects tanoak whilst conserving biodiversity: applying optimal control theory to a spatial simulation model of sudden oak death. bioRxiv https://doi.org/10.1101/773424
Sheehan H, Feng T, Walker-Hale N, Lopez-Nieves S, Pucker B, Guo R, Yim WC, Badgami R, Timoneda A, Zhao L, Tiley H, Copetti D, Sanderson MJ, Cushman JC, Moore MJ, Smith SA, Brockington SF. (2019) Evolution of l‐DOPA 4,5‐dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales. New Phytologist https://doi.org/10.1111/nph.16089
Allen-Sadler C, Thurston W, Meyer M, Nure E, Bacha N, Alemayehu Y, Stutt R, Safka D, Craig A, Derso E, Burgin L, Millington S, Hort MC, Hodson D, Gilligan CA. (2019) An early warning system to predict and mitigate wheat rust diseases in Ethiopia. Environmental Research Letters https://doi.org/10.1088/1748-9326/ab4034
Williams J, Schönlieb C, Swinfield T, Lee J, Cai X, Qie L, Coomes DA. (2019) 3D Segmentation of Trees Through a Flexible Multiclass Graph Cut Algorithm. IEEE Transactions on Geoscience and Remote Sensing https://doi.org/10.1109/TGRS.2019.2940146
Itakura AK, Chan KX, Atkinson N, Pallesen L, Wang L, Reeves G, Patena W, Caspari O, Roth R, Goodenough U, McCormick AJ, Griffiths H, Jonikas MC. (2019) A Rubisco-binding protein is required for normal pyrenoid number and starch sheath morphology in Chlamydomonas reinhardtii. PNAS https://doi.org/10.1073/pnas.1904587116
Lambing C, Choi K, Blackwell AR, Henderson IR. (2019) Chromatin Immunoprecipitation of Meiotically Expressed Proteins from Arabidopsis thaliana Flowers. Methods Mol Biol https://doi.org/10.1007/978-1-4939-9818-0_16
Lots including Brockington SF, Covshoff S, Hibberd JM, Kazamia E, Smith AG. (2019) One thousand plant transcriptomes and the phylogenomics of green plants. Nature https://doi.org/10.1038/s41586-019-1693-2
Harrison EL, Arce Cubas L, Gray JE, Hepworth C. (2019) The influence of stomatal morphology and distribution on photosynthetic gas exchange. The Plant Journal https://doi.org/10.1111/tpj.14560
Martí Ruiz MC, Jung HJ, Webb AAR. (2019) Circadian gating of dark‐induced increases in chloroplast‐ and cytosolic‐free calcium in Arabidopsis. New Phytologist https://doi.org/10.1111/nph.16280
Feng F, Sun J, Radhakrishnan GV, Lee T, Bozsóki Z, Fort S, Gavrin A, Gysel K, Thygesen MB, Andersen KR, Radutoiu S, Stougaard J, Oldroyd GED. (2019) A combination of chitooligosaccharide and lipochitooligosaccharide recognition promotes arbuscular mycorrhizal associations in Medicago truncatula. Nature Communications https://doi.org/10.1038/s41467-019-12999-5
Bailey-Serres J, Parker JE, Ainsworth EA, Oldroyd GED, Schroeder JI. (2019) Genetic strategies for improving crop yields. Nature https://doi.org/10.1038/s41586-019-1679-0
Román A, Golz JF, Webb AAR, Graham IA, Haydon MJ. (2019) Combining GAL4 GFP enhancer trap with split luciferase to measure spatiotemporal promoter activity in Arabidopsis. Arabidopsis Plant Journal https://doi.org/10.1111/tpj.14603
Tanentzap AJ, Igea J, Johnston MG, Larcombe MJ. (2019) Does evolutionary history correlate with contemporary extinction risk by influencing range size dynamics?. The American Naturalist https://doi.org/10.1086/707207
Airoldi CA, Hearn TJ, Brockington SF, Webb AAR, Glover BJ. (2019) TTG1 proteins regulate circadian activity as well as epidermal cell fate and pigmentation. Nature Plants https://doi.org/10.1038/s41477-019-0544-3
Bunbury F, Helliwell KE, Mehrshahi P, Davey MP, Salmon D, Holzer A, Smirnoff N, Smith AG. (2019) Physiological and molecular responses of a newly evolved auxotroph of Chlamydomonas to B12 deprivation. bioRxiv https://doi.org/10.1101/836635
Ladejobi O, Mackay IJ, Poland J, Praud S, Hibberd JM, Bentley AR. (2019) Reference Genome Anchoring of High-Density Markers for Association Mapping and Genomic Prediction in European Winter Wheat. Frontiers in Plant Science https://doi.org/10.3389/fpls.2019.01278
Sontowski R, Gorringe NJ, Pencs S, Schedl A, Touw AJ, van Dam NM. (2019) Same Difference? Low and High Glucosinolate Brassica rapa Varieties Show Similar Responses Upon Feeding by Two Specialist Root Herbivores. Frontiers in Plant Science https://doi.org/10.3389/fpls.2019.01451
Cornell SJ, Suprunenko YF, Finkelshtein D, Somervuo P, Ovaskainen O. (2019) A unified framework for analysis of individual-based models in ecology and beyond. Nature Communications https://doi.org/10.1038/s41467-019-12172-y
Laranjeira FF, Silva SXB, Murray-Watson RE, Soares ACF, Santos-Filho HP, Cunniffe NJ. (2019) Spatiotemporal dynamics and modelling support the case for area-wide management of citrus greasy spot in a Brazilian smallholder farming region. bioRxiv https://doi.org/10.1101/839431
Tanentzap AJ, Fitch A, Orland C, Emilson EJS, Yakimovich KM, Osterholz H, Dittmar T. (2019) Chemical and microbial diversity covary in fresh water to influence ecosystem functioning. PNAS https://doi.org/10.1073/pnas.1904896116
Kromdijk J, Glowacka K, Long SP. (2019) Photosynthetic efficiency and mesophyll conductance are unaffected in Arabidopsis thaliana aquaporin knock-out lines. Journal of Experimental Botany https://doi.org/10.1093/jxb/erz442
Orland C, Yakimovich KM, Mykytczuk NCS, Basiliko N, Tanentzap AJ. (2019) Think global, act local: The small‐scale environment mainly influences microbial community development and function in lake sediment. Limnology and Oceanography https://doi.org/10.1002/lno.11370
Kumar V, Chauhan S, Kumar M, Kumari R, Babu S, Yadav G. (2019) Chemical Curation of Lantana camara emissions across Native and Invaded Habitats. Zenodo https://doi.org/10.5281/zenodo.3558770
Tungadi T, Donnelly R, Qing L, Iqbal J, Murphy AM, Pate AE, Cunniffe NJ, Carr JP. (2019) Cucumber mosaic virus 2b proteins inhibit virus-induced aphid resistance in tobacco. Molecular Plant Pathology https://dx.doi.org/10.1111/mpp.12892
Hamelin FM, Allen LJS, Bokil VA, Gross LJ, Hilker FM, Jeger MJ, Manore CA, Power AG, Rúa MA, Cunniffe NJ. (2019) Coinfections by noninteracting pathogens are not independent and require new tests of interaction. PLOS Biology https://doi.org/10.1371/journal.pbio.3000551
Bogdziewicz M, Ascoli D, Hacket-Pain A, Koenig WD, Pearse I, Pesendorfer M, Satake A, Thomas P, Vacchiano G, Wohlgemuth T, Tanentzap A. (2019) From theory to experiments for testing the proximate mechanisms of mast seeding: an agenda for an experimental ecology. Ecology Letters https://doi.org/10.1111/ele.13442
Poon JSY, Le Fevre RE, Carr JP, Hanke DE, Murphy AM. (2019) Inositol hexakisphosphate biosynthesis underpins PAMP‐triggered immunity to Pseudomonas syringae pv. tomato in Arabidopsis thaliana but is dispensable for establishment of systemic acquired resistance. Molecular Plant Pathology https://doi.org/10.1111/mpp.12902
Previous years: