University of Dundee

Plant Sciences 2014

Ariyadasa, R., Mascher, M., Nussbaumer, T., Schulte, D., Frenkel, Z., Poursarebani, N., Zhou, R., Steuernagel, B., Gundlach, H., Taudien, S., Felder, M., Platzer, M., Himmelbach, A., Schmutzer, T., Hedley, P. E., Muehlbauer, G. J., Scholz, U., Korol, A., Mayer, K. F., Waugh, R., Langridge, P., Graner, A. and Stein, N. (2014) A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. Plant Physiology. 164, 412-423
doi.   10.1104/pp.113.228213
Pubmed.  24243933

Baker, K., Bayer, M., Cook, N., Dressig, S., Dhillon, T., Russell, J., Hedley, P. E., Morris, J., Ramsay, L., Colas, I., Waugh, R., Steffenson, B., Milne, I., Stephen, G., Marshall, D. and Flavell, A. J. (2014) The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression. Plant Journal. 79, 981-992
doi.  10.1111/Tpj.12600
Pubmed 24947331

Barakate, A., Higgins, J. D., Vivera, S., Stephens, J., Perry, R. M., Ramsay, L., Colas, I., Oakey, H., Waugh, R., Franklin, F. C., Armstrong, S. J. and Halpin, C. (2014) The synaptonemal complex protein ZYP1 is required for imposition of meiotic crossovers in barley. Plant Cell. 26, 729-740
doi.   10.1105/tpc.113.121269
Pubmed.  24563202

Bardou, F., Ariel, F., Simpson, C. G., Romero-Barrios, N., Laporte, P., Balzergue, S., Brown, J. W. and Crespi, M. (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Developmental Cell. 30, 166-176
doi.   10.1016/j.devcel.2014.06.017
Pubmed.  25073154

Bennett, A. E., Grussu, D., Kam, J., Caul, S. and Halpin, C. (2014) Plant lignin content altered by soil microbial community. New Phytologist
doi.   10.1111/nph.13171
Pubmed.  25389017

Boevink, P., McLellan, H., Bukharova, T., Engelhardt, S. and Birch, P. (2014) In vivo protein-protein interaction studies with BiFC: conditions, cautions, and caveats. Methods Mol Biol. 1127, 81-90
doi.   10.1007/978-1-62703-986-4_6
Pubmed.  24643553

Brodie, J., Williamson, C. J., Smale, D. A., Kamenos, N. A., Mieszkowska, N., Santos, R., Cunliffe, M., Steinke, M., Yesson, C., Anderson, K. M., Asnaghi, V., Brownlee, C., Burdett, H. L., Burrows, M. T., Collins, S., Donohue, P. J. C., Harvey, B., Foggo, A., Noisette, F., Nunes, J., Ragazzola, F., Raven, J. A., Schmidt, D. N., Suggett, D., Teichberg, M. and Hall-Spencer, J. M. (2014) The future of the northeast Atlantic benthic flora in a high CO2 world. Ecology and Evolution. 4, 2787-2798
doi.   10.1002/Ece3.1105
Pubmed.  25077027

Brown, S. P., Mead, A. J., Forgan, D. H., Raven, J. A. and Cockell, C. S. (2014) Photosynthetic potential of planets in 3:2 spin-orbit resonances. Int J Astrobiol. 13, 279-289
doi.   10.1017/S1473550414000068

Chapman, S., Stevens, L. J., Boevink, P. C., Engelhardt, S., Alexander, C. J., Harrower, B., Champouret, N., McGeachy, K., Van Weymers, P. S., Chen, X., Birch, P. R. and Hein, I. (2014) Detection of the virulent form of AVR3a from Phytophthora infestans following artificial evolution of potato resistance gene R3a. PLoS One. 9, e110158
doi.   10.1371/journal.pone.0110158
Pubmed.  25340613

De Maayer, P., Chan, W. Y., Rubagotti, E., Venter, S. N., Toth, I. K., Birch, P. R. and Coutinho, T. A. (2014) Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts. BMC Genomics. 15, 404
doi.   10.1186/1471-2164-15-404
Pubmed.  24884520

Fanesi, A., Raven, J. A. and Giordano, M. (2014) Growth rate affects the responses of the green alga Tetraselmis suecica to external perturbations. Plant Cell and Environment. 37, 512-519
doi.   10.1111/Pce.12176
Pubmed.  23927015

Giordano, M. and Raven, J. A. (2014) 00Nitrogen and sulfur assimilation in plants and algae. Aquat Bot. 118, 45-61
doi.   10.1016/j.aquabot.2014.06.012

Hemsley, P. A. (2014) Progress in understanding the mechanisms and functional importance of protein-membrane interactions in plants. New Phytologist. 204, 741-743
doi.   10.1111/nph.13072
Pubmed.  25367609

Hemsley, P. A. (2015) The importance of lipid modified proteins in plants. New Phytologist. 205, 476-489
doi.   10.1111/nph.13085
Pubmed.  25283240

Hemsley, P. A., Hurst, C. H., Kaliyadasa, E., Lamb, R., Knight, M. R., De Cothi, E. A., Steele, J. F. and Knight, H. (2014) The Arabidopsis mediator complex subunits MED16, MED14, and MED2 regulate mediator and RNA polymerase II recruitment to CBF-responsive cold-regulated genes. Plant Cell. 26, 465-484
doi.   10.1105/tpc.113.117796
Pubmed.  24415770

Houston, K., Russell, J., Schreiber, M., Halpin, C., Oakey, H., Washington, J. M., Booth, A., Shirley, N., Burton, R. A., Fincher, G. B. and Waugh, R. (2014) A genome wide association scan for (1,3;1,4)-beta-glucan content in the grain of contemporary 2-row Spring and Winter barleys. BMC Genomics. 15, 907
doi.   10.1186/1471-2164-15-907
Pubmed.  25326272

Jaouannet, M., Rodriguez, P. A., Thorpe, P., Lenoir, C. J., MacLeod, R., Escudero-Martinez, C. and Bos, J. I. (2014) Plant immunity in plant-aphid interactions. Frontiers in Plant Science. 5, 663
doi.   10.3389/fpls.2014.00663
Pubmed.  25520727

Jones, H. G. (2014) The use of indirect or proxy markers in plant physiology. Plant, Cell & Environment. 37, 1270-1272
doi.   10.1111/pce.12264
Pubmed.  24386877

Kamoun, S., Furzer, O., Jones, J. D., Judelson, H. S., Ali, G. S., Dalio, R. J., Roy, S. G., Schena, L., Zambounis, A., Panabieres, F., Cahill, D., Ruocco, M., Figueiredo, A., Chen, X. R., Hulvey, J., Stam, R., Lamour, K., Gijzen, M., Tyler, B. M., Grunwald, N. J., Mukhtar, M. S., Tome, D. F., Tor, M., Van Den Ackerveken, G., McDowell, J., Daayf, F., Fry, W. E., Lindqvist-Kreuze, H., Meijer, H. J., Petre, B., Ristaino, J., Yoshida, K., Birch, P. R. and Govers, F. (2014) The Top 10 oomycete pathogens in molecular plant pathology. Molecular Plant Pathology
doi.   10.1111/mpp.12190
Pubmed.  25178392

King, S. R., McLellan, H., Boevink, P. C., Armstrong, M. R., Bukharova, T., Sukarta, O., Win, J., Kamoun, S., Birch, P. R. and Banfield, M. J. (2014) Phytophthora infestans RXLR effector PexRD2 interacts with host MAPKKK epsilon to suppress plant immune signaling. Plant Cell. 26, 1345-1359
doi.   10.1105/tpc.113.120055
Pubmed.  24632534

Konecna, E., Safarova, D., Navratil, M., Hanacek, P., Coyne, C., Flavell, A., Vishnyakova, M., Ambrose, M., Redden, R. and Smykal, P. (2014) Geographical Gradient of the eIF4E Alleles Conferring Resistance to Potyviruses in Pea (Pisum) Germplasm. PLoS One. 9 doi.   ARTN e90394
doi 10.1371/journal.pone.0090394
Pubmed.  24609094

Liu, H., Bayer, M., Druka, A., Russell, J. R., Hackett, C. A., Poland, J., Ramsay, L., Hedley, P. E. and Waugh, R. (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics. 15, 104
doi.   10.1186/1471-2164-15-104
Pubmed.  24498911

Liu, W. Y. Y., Ridgway, H. J., James, T. K., James, E. K., Chen, W. M., Sprent, J. I., Young, J. P. W. and Andrews, M. (2014) Burkholderia sp Induces Functional Nodules on the South African Invasive Legume Dipogon lignosus (Phaseoleae) in New Zealand Soils. Microb Ecol. 68, 542-555
doi.   10.1007/s00248-014-0427-0

Mayer, K. F. X., Rogers, J., Dolezel, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A. J., Sourdille, P., Endo, T. R., Dolezel, J., Kubalakova, M., Cihalikova, J., Dubska, Z., Vrana, J., Sperkova, R., Simkova, H., Rogers, J., Febrer, M., Clissold, L., McLay, K., Singh, K., Chhuneja, P., Singh, N. K., Khurana, J., Akhunov, E., Choulet, F., Sourdille, P., Feuillet, C., Alberti, A., Barbe, V., Wincker, P., Kanamori, H., Kobayashi, F., Itoh, T., Matsumoto, T., Sakai, H., Tanaka, T., Wu, J. Z., Ogihara, Y., Handa, H., Pozniak, C., Maclachlan, P. R., Sharpe, A., Klassen, D., Edwards, D., Batley, J., Olsen, O. A., Sandve, S. R., Lien, S., Steuernagel, B., Wulff, B., Caccamo, M., Ayling, S., Ramirez-Gonzalez, R. H., Clavijo, B. J., Steuernagel, B., Wright, J., Pfeifer, M., Spannagl, M., Mayer, K. F. X., Martis, M. M., Akhunov, E., Choulet, F., Mayer, K. F. X., Mascher, M., Chapman, J., Poland, J. A., Scholz, U., Barry, K., Waugh, R., Rokhsar, D. S., Muehlbauer, G. J., Stein, N., Gundlach, H., Zytnicki, M., Jamilloux, V., Quesneville, H., Wicker, T., Mayer, K. F. X., Faccioli, P., Colaiacovo, M., Pfeifer, M., Stanca, A. M., Budak, H., Cattivelli, L., Glover, N., Martis, M. M., Choulet, F., Feuillet, C., Mayer, K. F. X., Pfeifer, M., Pingault, L., Mayer, K. F. X., Paux, E., Spannagl, M., Sharma, S., Mayer, K. F. X., Pozniak, C., Appels, R., Bellgard, M., Chapman, B., Pfeifer, M., Pfeifer, M., Sandve, S. R., Nussbaumer, T., Bader, K. C., Choulet, F., Feuillet, C., Mayer, K. F. X., Akhunov, E., Paux, E., Rimbert, H., Wang, S. C., Poland, J. A., Knox, R., Kilian, A., Pozniak, C., Alaux, M., Alfama, F., Couderc, L., Jamilloux, V., Guilhot, N., Viseux, C., Loaec, M., Quesneville, H., Rogers, J., Dolezel, J., Eversole, K., Feuillet, C., Keller, B., Mayer, K. F. X., Olsen, O. A., Praud, S. and Iwgsc. (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. 345 Artn 1251788
Doi 10.1126/Science.1251788
Pubmed.  25035500

Mendiondo, G. M., Medhurst, A., van Roermund, C. W., Zhang, X., Devonshire, J., Scholefield, D., Fernandez, J., Axcell, B., Ramsay, L., Waterham, H. R., Waugh, R., Theodoulou, F. L. and Holdsworth, M. J. (2014) Barley has two peroxisomal ABC transporters with multiple functions in beta-oxidation. Journal of Experimental Botany. 65, 4833-4847
doi.   10.1093/jxb/eru243
Pubmed.  24913629

Mitra, A., Flynn, K. J., Burkholder, J. M., Berge, T., Calbet, A., Raven, J. A., Graneli, E., Glibert, P. M., Hansen, P. J., Stoecker, D. K., Thingstad, F., Tillmann, U., Vage, S., Wilken, S. and Zubkov, M. V. (2014) The role of mixotrophic protists in the biological carbon pump. Biogeosciences. 11, 995-1005
doi.   10.5194/bg-11-995-2014

Munoz-Amatriain, M., Cuesta-Marcos, A., Endelman, J. B., Comadran, J., Bonman, J. M., Bockelman, H. E., Chao, S., Russell, J., Waugh, R., Hayes, P. M. and Muehlbauer, G. J. (2014) The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One. 9, e94688
doi.   10.1371/journal.pone.0094688
Pubmed.  24732668

Marcussen, Thomas; Sandve, Simen R; Heier, Lise; Spannagl, Manuel; Pfeifer, Matthias; Jakobsen, Kjetill S; Wulff, Brande BH; Steuernagel, Burkhard; Mayer, Klaus FX; Olsen, Odd-Arne; Ancient hybridizations among the ancestral genomes of bread wheat. Science 345 6194 1250092 2014

O'Malley-James, J. T., Cockell, C. S., Greaves, J. S. and Raven, J. A. (2014) Swansong biospheres II: the final signs of life on terrestrial planets near the end of their habitable lifetimes. Int J Astrobiol. 13, 229-243
doi.   10.1017/S1473550413000426

Petrillo, E., Godoy Herz, M. A., Fuchs, A., Reifer, D., Fuller, J., Yanovsky, M. J., Simpson, C., Brown, J. W., Barta, A., Kalyna, M. and Kornblihtt, A. R. (2014) A chloroplast retrograde signal regulates nuclear alternative splicing. Science. 344, 427-430
doi.   10.1126/science.1250322
Pubmed.  24763593

Pritchard, L. and Birch, P. R. (2014) The zigzag model of plant-microbe interactions: is it time to move on? Molecular Plant Pathology. 15, 865-870
doi.   10.1111/mpp.12210
Pubmed.  25382065

Raczynska, K. D., Stepien, A., Kierzkowski, D., Kalak, M., Bajczyk, M., McNicol, J., Simpson, C. G., Szweykowska-Kulinska, Z., Brown, J. W. and Jarmolowski, A. (2014) The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana. Nucleic Acids Res. 42, 1224-1244
doi.   10.1093/nar/gkt894
Pubmed.  24137006

Randall, E., Young, V., Sierotzki, H., Scalliet, G., Birch, P. R., Cooke, D. E., Csukai, M. and Whisson, S. C. (2014) Sequence diversity in the large subunit of RNA polymerase I contributes to Mefenoxam insensitivity in Phytophthora infestans. Molecular Plant Pathology. 15, 664-676
doi.   10.1111/mpp.12124
Pubmed.  24521429

Rataj, K. and Simpson, G. G. (2014) Message ends: RNA 3' processing and flowering time control. Journal of Experimental Botany. 65, 353-363
doi.   10.1093/jxb/ert439
Pubmed.  24363425

Raven, J. A. (2014) Speedy small stomata? Journal of Experimental Botany. 65, 1415-1424
doi.   10.1093/Jxb/Eru032

Raven, J. A. and Beardall, J. (2014) CO2 concentrating mechanisms and environmental change. Aquat Bot. 118, 24-37
doi.   10.1016/j.aquabot.2014.05.008

Raven, J. A., Beardall, J. and Giordano, M. (2014) Energy costs of carbon dioxide concentrating mechanisms in aquatic organisms. Photosynthesis Research. 121, 111-124
doi.   DOI 10.1007/s11120-013-9962-7
Pubmed.  24390639

Raven, J. A. and Doblin, M. A. (2014) Active water transport in unicellular algae: where, why, and how. Journal of Experimental Botany. 65, 6279-6292
doi.   10.1093/jxb/eru360
Pubmed.  25205578

Raven, J. A. and Edwards, D. (2014) Photosynthesis in Early Land Plants: Adapting to the Terrestrial Environment. Adv Photosynth Resp. 37, 29-58
doi.   10.1007/978-94-007-6988-5_3

Rodriguez, P. A., Hogenhout, S. A. and Bos, J. I. (2014) Leaf-disc assay based on transient over-expression in Nicotiana benthamiana to allow functional screening of candidate effectors from aphids. Methods Mol Biol. 1127, 137-143
doi.   10.1007/978-1-62703-986-4_11
Pubmed.  24643558

Rodriguez, P. A., Stam, R., Warbroek, T. and Bos, J. I. (2014) Mp10 and Mp42 from the aphid species Myzus persicae trigger plant defenses in Nicotiana benthamiana through different activities. Molecular Plant-Microbe Interactions : MPMI. 27, 30-39
doi.   10.1094/MPMI-05-13-0156-R
Pubmed.  24006884

Russell, J., van Zonneveld, M., Dawson, I. K., Booth, A., Waugh, R. and Steffenson, B. (2014) Genetic diversity and ecological niche modelling of wild barley: refugia, large-scale post-LGM range expansion and limited mid-future climate threats? PLoS One. 9, e86021
doi.   10.1371/journal.pone.0086021
Pubmed.  24505252

Sanchez-Baracaldo, P., Ridgwell, A. and Raven, J. A. (2014) A Neoproterozoic Transition in the Marine Nitrogen Cycle. Current Biology. 24, 652-657
doi.   10.1016/j.cub.2014.01.041
Pubmed.  24583016

Schlaeppi, K. and Bulgarelli, D. (2014) The plant microbiome at work. Molecular Plant-Microbe Interactions : MPMI
doi.   10.1094/MPMI-10-14-0334-FI
Pubmed.  25514681

Schreiber, M., Wright, F., MacKenzie, K., Hedley, P. E., Schwerdt, J. G., Little, A., Burton, R. A., Fincher, G. B., Marshall, D., Waugh, R. and Halpin, C. (2014) The barley genome sequence assembly reveals three additional members of the CslF (1,3;1,4)-beta-glucan synthase gene family. PLoS One. 9, e90888
doi.   10.1371/journal.pone.0090888
Pubmed.  24595438

Schurch, N. J., Cole, C., Sherstnev, A., Song, J., Duc, C., Storey, K. G., McLean, W. H., Brown, S. J., Simpson, G. G. and Barton, G. J. (2014) Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs. PLoS One. 9, e94270
doi.   10.1371/journal.pone.0094270
Pubmed.  24722185

Segretin, M. E., Pais, M., Franceschetti, M., Chaparro-Garcia, A., Bos, J. I., Banfield, M. J. and Kamoun, S. (2014) Single amino acid mutations in the potato immune receptor R3a expand response to Phytophthora effectors. Molecular Plant-Microbe Interactions : MPMI. 27, 624-637
doi.   10.1094/MPMI-02-14-0040-R
Pubmed.  24678835

Simpson, C. G., Lewandowska, D., Liney, M., Davidson, D., Chapman, S., Fuller, J., McNicol, J., Shaw, P. and Brown, J. W. (2014) Arabidopsis PTB1 and PTB2 proteins negatively regulate splicing of a mini-exon splicing reporter and affect alternative splicing of endogenous genes differentially.  New Phytologist. 203, 424-436
doi.   10.1111/nph.12821
Pubmed.  24749484

Sulpice, R., Ishihara, H., Schlereth, A., Cawthray, G. R., Encke, B., Giavalisco, P., Ivakov, A., Arrivault, S., Jost, R., Krohn, N., Kuo, J., Laliberte, E., Pearse, S. J., Raven, J. A., Scheible, W. R., Teste, F., Veneklaas, E. J., Stitt, M. and Lambers, H. (2014) Low levels of ribosomal RNA partly account for the very high photosynthetic phosphorus-use efficiency of Proteaceae species. Plant Cell and Environment. 37, 1276-1298
doi.   10.1111/Pce.12240

Szabo, M., Parker, K., Guruprasad, S., Kuzhiumparambil, U., Lilley, R. M., Tamburic, B., Schliep, M., Larkum, A. W. D., Schreiber, U., Raven, J. A. and Ralph, P. J. (2014) Photosynthetic acclimation of Nannochloropsis oculata investigated by multi-wavelength chlorophyll fluorescence analysis. Bioresource Technology. 167, 521-529
doi.   10.1016/j.biortech.2014.06.046
Pubmed.  25016367

Tamburic, B., Guruprasad, S., Radford, D. T., Szabo, M., Lilley, R. M., Larkum, A. W. D., Franklin, J. B., Kramer, D. M., Blackburn, S. I., Raven, J. A., Schliep, M. and Ralph, P. J. (2014) The Effect of Diel Temperature and Light Cycles on the Growth of Nannochloropsis oculata in a Photobioreactor Matrix. PLoS One. 9.   ARTN e86047
doi 10.1371/journal.pone.0086047
Pubmed.  24465862

Tilston, E. L., Halpin, C. and Hopkins, D. W. (2014) Simultaneous down-regulation of enzymes in the phenylpropanoid pathway of plants has aggregated effects on rhizosphere microbial communities. Biol Fert Soils. 50, 455-463
doi.   10.1007/s00374-013-0862-y

Tondelli, A., Pagani, D., Ghafoori, I. N., Rahimi, M., Ataei, R., Rizza, F., Flavell, A. J. and Cattivelli, L. (2014) Allelic variation at Fr-H1/Vrn-H1 and Fr-H2 loci is the main determinant of frost tolerance in spring barley.  Environ Exp Bot. 106, 148-155
doi.   10.1016/j.envexpbot.2014.02.014

Vega-Arreguin, J. C., Jalloh, A., Bos, J. I. and Moffett, P. (2014) Recognition of an Avr3a homologue plays a major role in mediating nonhost resistance to Phytophthora capsici in Nicotiana species. Molecular Plant-Microbe interactions : MPMI. 27, 770-780
doi.   10.1094/MPMI-01-14-0014-R
Pubmed.  24725207

Werner, G. D., Cornwell, W. K., Sprent, J. I., Kattge, J. and Kiers, E. T. (2014) A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. Nature Coms. 5, 4087
doi.   10.1038/ncomms5087
Pubmed.  24912610

Wiesel, L., Newton, A. C., Elliott, I., Booty, D., Gilroy, E. M., Birch, P. R. and Hein, I. (2014) Molecular effects of resistance elicitors from biological origin and their potential for crop protection. Frontiers in Plant Science. 5, 655
doi.   10.3389/fpls.2014.00655
Pubmed.  25484886

Wu, X. M., Hornyik, C., Bayer, M., Marshall, D., Waugh, R. and Zhang, R. X. (2014) In silico identification and characterization of conserved plant microRNAs in barley. Cent Eur J Biol. 9, 841-852
doi.   10.2478/s11535-014-0308-z

Xu, Y., Plechanovova, A., Simpson, P., Marchant, J., Leidecker, O., Kraatz, S., Hay, R. T. and Matthews, S. J. (2014) Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4. Nature Coms. 5, 4217
doi.   10.1038/ncomms5217
Pubmed.  24969970

Zheng, X., McLellan, H., Fraiture, M., Liu, X., Boevink, P. C., Gilroy, E. M., Chen, Y., Kandel, K., Sessa, G., Birch, P. R. and Brunner, F. (2014) Functionally redundant RXLR effectors from Phytophthora infestans act at different steps to suppress early flg22-triggered immunity. PLoS Pathog. 10, e1004057
doi.   10.1371/journal.ppat.1004057
Pubmed.  24763622