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2016

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:

2016

Thompson RN, Cobb RC, Gilligan CA, Cunniffe NJ. (2016) Management of invading pathogens should be informed by epidemiology rather than administrative boundaries. Ecological Modelling http://dx.doi.org/10.1016/j.ecolmodel.(2015).12.014 

Harris CJ, Baulcombe DC. (2015) Chlorophyll Content Assay to Quantify the Level of Necrosis Induced by Different R Gene / Elicitor Combinations after Transient Expression. Bio-Protocol 

Lamb A, Green R, Bateman I, Broadmeadow M, Bruce T, Burney J, Carey P, Chadwick D, Crane E, Field R, Goulding K, Griffiths H, Hastings A, Kasoar T, Kindred D, Phalan B, Pickett J, Smith P, Wall E, zu Ermgassen EKHJ, Balmford A. (2016) The potential for land sparing to offset greenhouse gas emissions from agriculture. Nature Climate Change http://dx.doi.org/10.1038/nclimate2910 

Kunstler G, Falster D, Coomes DA, et al. (2015) Plant functional traits have globally consistent effects on competition.  Nature http://dx.doi.org/10.1038/nature16476 

Lewsey MG, Hardcastle TJ, Melnyn CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR. (2016) Mobile small RNAs regulate genome-wide DNA methylation. PNAS http://dx.doi.org/10.1073/pnas.1515072113 

Williams BP, Burgess SJ, Reyna-Llorens I, Knerova J, Aubry S, Stanley S, Hibberd JM. (2016) An untranslated cis-element regulates the accumulation of multiple C4 enzymes in Gynandropsis gynandra mesophyll cells. The Plant Cell http://dx.doi.org/10.1105/tpc.15.00570 

Lee W-S, Fu S-F, Li Z, Murphy AM, Dobson EA, Garland L, Chalavadi SR, Lewsey MG, Nelson RS, Carr JP (2016) Salicylic acid treatment and expression of an RNA-dependent RNA polymerase 1 transgene inhibit lethal symptoms and meristem invasion during tobacco mosaic virus infection in Nicotiana benthamiana. BMC Plant Biology http://dx.doi.org/10.1186/s12870-016-0705-8 

Mingot A, Valli A, Rodamilans B, San León, David, Baulcombe DC, García JA, López-Moya JJ (2016) The P1N-PISPO Trans-frame Gene of Sweet Potato Feathery Mottle Potyvirus is Produced During Virus Infection and Functions as RNA Silencing Suppressor.  Journal of Virology http://dx.doi.org/10.1128/JVI.02360-15  

Jucker T. Avăcăriței D, Bărnoaiea I, Duduman G, Bouriaud O, Coomes DA. (2016) Climate modulates the effects of tree diversity on forest productivity. Journal of Ecology http://dx.doi.org/10.1111/1365-2745.12522 

Aubry S, Aresheva O, Reyna-Llorens I, Smith-Unna R, Hibberd JM, Genty B. (2016) A specific transcriptome signature for guard cells from the C4 plant Gynandropsis gynandra Plant Physiology http://dx.doi.org/10.1104/pp.15.01203 

Grant PK, Dalchau N, Brown, JR, Federici F, Rudge TJ, Yordanov B, Patange O, Philips A, Haseloff J. (2016) Orthogonal intercellular signaling for programmed spatial behavior Molecular Systems Biology http://dx.doi.org/10.15252/msb.20156590 

Simonson W, Ruiz-Benito P, Valladares F & Coomes D. (2016) Modelling above ground carbon dynamics using multi-temporal airborne lidar: insights from a Mediterranean woodland. Biogeosciences http://dx.doi.org/10.5194/bg-13-961-2016 

Abdul-Awal, S.M., Hotta, C.T., Davey, M.P., Dodd, A.N., Smith A.G. and Webb, A.A.R. (2016) NO-mediated [Ca2+]cyt increases depend on ADP-ribosyl cyclase activity in Arabidopsis.  Plant Physiology http://dx.doi.org/10.1104/pp.15.01965 

Thompson RN, Gilligan CA, Cunniffe NJ (2016) Detecting Presymptomatic Infection is Necessary to Forecast Major Epidemics in the Earliest Stages of Infectious Disease Outbreaks PLOS Computational Biology http://dx.doi.org/10.1371/journal.pcbi.1004836 

Sawers RJH, Svane SF, Quan C, Gronlund M, Wozniak B, Nigussie M, Mueller M, Gonzalez-Munoz E, Chavez Montes R, Baxter I, Goudet J, Jakobsen I, Paszkowski U (2016) Outcome variation in maize mycorrhizal symbiosis bioRxiv http://dx.doi.org/10.1101/042028 

Gouil Q, Novák O, and Baulcombe DC. (2016) SLTAB2 is the paramutated SULFUREA locus in tomato Journal of Experimental Botany http://dx.doi.org/10.1093/jxb/erw096 

Hunter LJR, Brockington SF, Murphy AM, Pate AE, Gruden K, MacFarlane SA, Palukaitis P and Carr JP. (2016) RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases Scientific Reports http://dx.doi.org/10.1038/srep23082 

Royles J, Amesbury MJ, Roland TP, Jones GD, Convey P, Griffiths H, Hodgson DA, Charman DJ. (2016) Moss stable isotopes (13C, 18O) and testate amoebae reflect environmental inputs and microclimate along a latitudinal gradient on the Antarctic Peninsula. Springer. http://dx.doi.org/10.1007/s00442-016-3608-3 

Glover B. (2016) More than the (human) eye can see: the regulation of floral UV absorbance. Flowering Highlights. (Journal of Experimental Botany) 

Emms DM, Covshoff S, Hibberd JM, Kelly S. (2016) Independent and parallel evolution of new genes by gene duplication in two origins of C4 photosynthesis provides new insight into the mechanism of phloem loading in C4 species. Molecular Biology and Evolution http://dx.doi.org/10.1093/molbev/msw057 

van der Plas F, Manning P, Allan E, Scherer-Lorenzen M, Verheyen K, Wirth C, Zavala MA, Hector A, Ampoorter E, Baeten L, Barbaro L, Bauhus J, Benavides R, Benneter A, Berthold F, Bonal D, Bouriaud O, Bruelheide H, Bussotti F, Carnol M, Castagneyrol B, Charbonnier Y, Coomes D, Coppi A, Bastias CC, Muhie Dawud S, De Wandeler H, Domisch T, Finer L, Gessler A, Granier A, Crossiord C, Guyot V, Hattenschwiler S, Jactel H, Jaroszewicz B, Joly F, Jucker T, Koricheva J, Milligan H, Muller S, Muys B, Nguyen D, Pollastrini M, Raulund-Rasmussen K, Selvi F, Stenlid J, Valladares F, Vesterdal L, Zielinski D, Fischer M. (2016) Jack-of-all-trades effects drive biodiversity–ecosystem multifunctionality relationships in European forests  http://dx.doi.org/10.1038/ncomms11109 

Helliwell KE, Lawrence AD, Holzer A, Kudahl UJ, Sasso S, Kräutler B, Scanlan DJ, Warren MJ, Smith AG. (2016) Cyanobacteria and Eukaryotic Algae Use Different Chemical Variants of Vitamin B12  http://dx.doi.org/10.1016/j.cub.2016.02.041 

 Cunniffe NJ, Cobb RRC, Meentemeyer RK, Rizzo DM, Gilligan CA.  (2016) Modelling when, where and how to manage a forest epidemic, motivated by sudden oak death in California PNAS http://dx.doi.org/10.1073/pnas.1602153113 

Bennett T, Hines G, van Rongen M, Waldie T, Sawchuk MG, Scarpella E, Ljung K, Leyser O.  (2016) Connective auxin transport in the shoot facilitates communication between shoot apices Plos Biol http://dx.doi.org/10.1371/journal.pbio.1002446 

Valli AA, Santos BACM, Hnatova S, Bassett AR, Molnar AM, Chung BY, Baulcombe DC (2016) Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs  Genome Res. http://dx.doi.org/10.1101/gr.199703.115 

Monks A, Monk JM, Tanentzap AJ (2016) Resource limitation underlying multiple masting models makes mast seeding sensitive to future climate change. New Phytologist http://dx.doi.org/10.1111/nph.13817 

Gonzalez-Jorge S, Mehrshahi P, Magallanes-Lundback M, Lipka AE, Angelovici R, Gore MA, DellaPenna D. (2016) ZEAXANTHIN EPOXIDASE activity potentiates carotenoid degradation in maturing Arabidopsis seed. Plant Physiol. http://dx.doi.org/10.1104/pp.16.00604 

Mackinder LCM, Meyer MT, Mettler-Altmann T, Chen VK, Mitchell MC, Caspari O, Freeman Rosenzweig ES, Pallesen L, Reeves G, Itakura A, Roth R, Sommer F, Geimer S, Mühlhaus T, Schroda M, Goodenough U, Stitt M, Griffiths H, Jonikas MC.  (2016) A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle PNAS http://dx.doi.org/10.1073/pnas.1522866113 

Meyer MT, McCormick AJ, Griffiths H (2016) Will an algal CO 2-concentrating mechanism work in higher plants? Current Opinion in Plant Biology http://dx.doi.org/10.1016/j.pbi.(2016).04.009 

Olspert A, Carr JP, Firth AE. (2016) Mutational analysis of the Potyviridae transcriptional slippage site utilized for expression of the P3N-PIPO and P1N-PISPO proteins Nucleic Acids Research http://dx.doi.org/10.1093/nar/gkw441 

Carignano A, Junyang J, Yuan Y, Gonçalves J, Webb A.  (2016) Research Data Supporting" Nu gap identifies systems alterations in the Arabidopsis thaliana circadian clock" http://dx.doi.org/10.17863/CAM.5 

Szkokan-Emilson EJ, Kielstra BW, Arnott SE, Watmough SA, Gunn JM, Tanentzap AJ.  (2016) Dry conditions disrupt terrestrial-aquatic linkages in northern catchments. Global Change Biology. http://dx.doi.org/10.1111/gcb.13361 

Smith-Unna R, Boursnell C, Patro R, Hibberd J, Kelly S. (2016) TransRate: reference free quality assessment of de novo transcriptome assemblies Genome Research http://dx.doi.org/10.1101/gr.196469.115 

Jucker T, Caspersen J, Chave J, Antin C, Barbier N, Bongers F, Dalponte M, van Ewijk KY, Forrester DI, Haeni M, Higgins SI, Holdaway RJ, Iida Y, Lorimer C, Marshall PL, Momo S, Moncrieff GR, Ploton P, Poorter L, Rahman KA, Schlund M, Sonké B, Sterck FJ, Trugman AT, Usoltsev VA, Vanderwel MC, Waldner P, Wedeux BMM, Wirth C, Wöll H, Woods M, Xiang W, Zimmermann NE and Coomes DA (2016) Allometric equations for integrating remote sensing imagery into forest monitoring programmes Glob Change Biol http://dx.doi.org/10.1111/gcb.13388 

Choi K, Reinhard C, Serra H, Ziolkowski PA, Underwood CJ, Zhao X, Hardcastle TJ, Yelina NE, Griffin C, Jackson M, Mézard C, McVean G, Copenhaver GP, Henderson IR.  (2016) Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLOS http://dx.doi.org/10.1371/journal.pgen.1006179 

Groen SC, Jiang S, Murphy AM, Cunniffe NJ, Westwood JH, Davey MP, Bruce TJA, Caulfield JC, Furzer OJ, Reed A, Robinson SI, Miller E, Davis CN, Pickett JA, Whitney HM, Glover BJ, Carr JP. (2016) Virus Infection of Plants Alters Pollinator Preference: A Payback for Susceptible Hosts? PLOS Pathogens. PLOS Pathogens http://dx.doi.org/10.1371/journal.ppat.1005790 

Hardcastle, TJ, Lewsey MG. (2016) Mobile small RNAs and their role in regulating cytosine methylation of DNA. RNA Biology RNA Biology http://dx.doi.org/10.1080/15476286.2016.1218591 

Tanentzap A.J, Lee W G (2016) Evolutionary conservatism explains increasing relatedness of plant communities along a flooding gradient. New Phytologist http://dx.doi.org/10.1111/nph.14167

Wilkins KA, Matthus E, Swarbreck SM, Davies JM.  (2016) Calcium-mediated abiotic stress signalling in roots.  Frontiers in Plant Sciences http://dx.doi.org/10.3389/fpls.2016.01296 

Hibberd JM, Furbank RT. (2016) In retrospect: Fifty years of C4 photosynthesis Nature http://dx.doi.org/10.1038/538177b

Jurić I, González-Pérez V, Hibberd JM, Edwards G, Burroughs NJ (2016) Size matters for single-cell C4 photosynthesis in Bienertia Journal of Experimental Botany http://dx.doi.org/10.1093/jxb/erw374 

Burgess SJ, Granero-Moya I, Grangé-Guermente MJ, Boursnell C, Terry MJ and Hibberd JM (2016) Ancestral light and chloroplast regulation form the foundations for C4 gene expression Nature Plants http://dx.doi.org/10.1038/NPLANTS.2016.161 

Brandt AJ, Tanentzap AJ, Leopold DR, Heenan PB, Fukami T, WG Lee (2016) Precipitation alters the strength of evolutionary priority effects in forest community assembly of pteridophytes and angiosperms.  Journal of Ecology http://dx.doi.org/10.1111/1365-2745.12640 

Liang J, Crowther TW, Picard N, Wiser S, Zhou M, Alberti G,Schulze E, McGuire AD, Bozzato F, Pretzsch H, de-Miguel S, Paquette A, Hérault B, Scherer-Lorenzen M, Barrett CB, Glick HB, Hengeveld GM, Nabuurs G, Pfautsch S, Viana H, Vibrans AC, Ammer C, Schall P, Verbyla D, Tchebakova N, Fischer M, Watson JV, Chen HYH, Lei X, Schelhaas M, Lu H, Gianelle D, Parfenova EI, Salas C, Lee E, Lee B, Kim HS, Bruelheide H, Coomes DA, Piotto D, Sunderland T, Schmid B, Gourlet-Fleury S, Sonké B, Tavani R, Zhu J, Brandl S, Vayreda J, Kitahara F, Searle EB, Neldner VJ, Ngugi MR, Baraloto C, Frizzera L, Bałazy R, Oleksyn J, Zawiła-Niedźwiecki T, Bouriaud O, Bussotti F, Finér L, Jaroszewicz B, Jucker T, Valladares F, Jagodzinski AM, Peri PL, Gonmadje C, Marthy W, O’Brien T, Martin EH, Marshall AR, Rovero F, Bitariho R, Niklaus PA, Alvarez-Loayza P, Chamuya N, Valencia R, Mortier F, Wortel V, Engone-Obiang NL, Ferreira LV, Odeke DE, Vasquez RM, Lewis SL, Reich PB. (2016) Positive biodiversity-productivity relationship predominant in global forests Science http://dx.doi.org/10.1126/science.aaf8957 

Hibberd JM, Furbank RT. (2016) Wheat genomics: Seeds of C4 photosynthesis Nature Plants http://dx.doi.org/10.1038/NPLANTS.(2016).172

Ladejobia O, Elderfield J, Gardnera KA, Gaynor C, Hickey J, Hibberd JM, Mackay IJ, Bentley AR (2016) Maximizing the potential of multi-parental crop populations Science Direct http://dx.doi.org/10.1016/j.atg.2016.10.002 

Vignolini S, Gregory T, Kolle M, Lethbridge A, Moyroud E, Steiner U, Glover BJ, Vukusic P, Rudall PJ. (2016) Structural colour from helicoidal cell-wall architecture in fruits of Margaritaria nobilis. Journal of the Royal Society Interface. http://dx.doi.org/10.1098/rsif.2016.0645 

Bennett T, Liang Y, Seale M, Ward S, Müller D, Leyser O.  (2016) Strigolactone regulates shoot development through a core signalling pathway Biology Open. http://dx.doi.org/10.1242/bio.021402 

Tanner EVJ, Sheldrake MWA, Turner BLT (2016) Changes in soil carbon and nutrients following 6 years of litter removal and addition in a tropical semi-evergreen rain forest  Biogeosciences http://dx.doi.org/10.5194/bg-13-6183-2016 

Nuñez IN, Matute TF, Del Valle I, Kan A, Choksi A, Endy D, Haseloff J, Rudge T, Federici F. (2016) Artificial symmetry-breaking for morphogenetic engineering bacterial colonies ACS Synth. Biol http://dx.doi.org/10.1021/acssynbio.6b00149 

Reyna-Llorens I, Burgess SJ, Williams BP, Stanley S, Boursnell C, Hibberd JM. (2016) Ancient coding sequences underpin the spatial patterning of gene expression in C4 leaves bioRxiv http://dx.doi.org/10.1101/085795 

Kumpers BMC, Burgess SJ, Reyna-Llorens I, Smith-Unna R, Boursnell C, Hibberd JM. (2016) Shared characteristics underpinning C4 leaf maturation derived from analysis of multiple C3 and C4 species of Flaveria bioRxiv http://dx.doi.org/10.1101/088153 

Angelovici R, Batushansky A, Deason N, Gonzalez-Jorge S, Gore MA, Fait A, DellaPenna D (2016) Network-guided GWAS improves identification of genes affecting free amino acids Plant Physiol. http://dx.doi.org/10.1104/pp.16.01287  

Moyroud E, Glover BJ (2016) The physics of pollinator attraction New Phytologist http://dx.doi.org/10.1111/nph.14312 

Solly JE, Cunniffe NJ, Harrison CJ (2016) Regional Growth Rate Differences Specified by Apical Notch Activities Regulate Liverwort Thallus Shape Current Biology http://dx.doi.org/10.1016/j.cub.2016.10.056 

Holdaway RJ, Easdale TA, Carswell FE, Richardson SJ, Peltzer DA, Mason NWH, Brandon AM, Coomes DA. (2016) Nationally Representative Plot Network Reveals Contrasting Drivers of Net Biomass Change in Secondary and Old-Growth Forests Ecosystems http://dx.doi.org/10.1007/s10021-016-0084-x

Gouil Q, Baulcombe DC. (2016) DNA Methylation Signatures of the Plant Chromomethyltransferases PLOS Genetics http://dx.doi.org/10.1371/journal.pgen.1006526 

Reeves G, Grange-Guermente MJ, Hibberd JM (2016) Regulatory gateways for cell-specific gene expression in C4 leaves with Kranz anatomy Journal of Experimental Botany http://dx.doi.org/10.1093/jxb/erw438   

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