University of Dundee

Plant Sciences 2015

Baker, K., Dhillon, T., Colas, I., Cook, N., Milne, I., Milne, L., Bayer, M. and Flavell, A. J. (2015) Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance. Plant J. 84, 111-124
d.o.i: 10.1111/tpj.12963
PMC: 26255869

Bennett, A. E., Grussu, D., Kam, J., Caul, S. and Halpin, C. (2015) Plant lignin content altered by soil microbial community. New Phytol. 206, 166-174
d.o.i: 10.1111/nph.13171
PMC: 25389017

Brooker, R. W., Bennett, A. E., Cong, W. F., Daniell, T. J., George, T. S., Hallett, P. D., Hawes, C., Iannetta, P. P., Jones, H. G., Karley, A. J., Li, L., McKenzie, B. M., Pakeman, R. J., Paterson, E., Schob, C., Shen, J., Squire, G., Watson, C. A., Zhang, C., Zhang, F., Zhang, J. and White, P. J. (2015) Improving intercropping: a synthesis of research in agronomy, plant physiology and ecology. New Phytol. 206, 107-117
PMC: 25866856

Brown, J. W., Simpson, C. G., Marquez, Y., Gadd, G. M., Barta, A. and Kalyna, M. (2015) Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts. Plant Cell. 27, 2083-2087
d.o.i: 10.1105/tpc.15.00572
Pubmed: 4568512
PMC: 26286536

Bulgarelli, D., Garrido-Oter, R., Munch, P. C., Weiman, A., Droge, J., Pan, Y., McHardy, A. C. and Schulze-Lefert, P. (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe. 17, 392-403
d.o.i: 10.1016/j.chom.2015.01.011
Pubmed: 4362959
PMC: 25732064

Calixto, C. P., Waugh, R. and Brown, J. W. (2015) Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes. J Mol Evol. 80, 108-119
d.o.i: 10.1007/s00239-015-9665-0
Pubmed: 4320304
PMC: 25608480

Chapman, J. A., Mascher, M., Buluc, A., Barry, K., Georganas, E., Session, A., Strnadova, V., Jenkins, J., Sehgal, S., Oliker, L., Schmutz, J., Yelick, K. A., Scholz, U., Waugh, R., Poland, J. A., Muehlbauer, G. J., Stein, N. and Rokhsar, D. S. (2015) A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol. 16, 26
d.o.i: 10.1186/s13059-015-0582-8
Pubmed: 4373400
PMC: 25637298

Dawson, I. K., Russell, J., Powell, W., Steffenson, B., Thomas, W. T. and Waugh, R. (2015) Barley: a translational model for adaptation to climate change. New Phytol. 206, 913-931
d.o.i: 10.1111/nph.13266
PMC: 25605349

Du, Y., Mpina, M. H., Birch, P. R., Bouwmeester, K. and Govers, F. (2015) Phytophthora infestans RXLR Effector AVR1 Interacts with Exocyst Component Sec5 to Manipulate Plant Immunity. Plant Physiol. 169, 1975-1990
d.o.i: 10.1104/pp.15.01169
Pubmed: 4634092
PMC: 26336092

Edwards, D., Cherns, L. and Raven, J. A. (2015) Could land-based early photosynthesizing ecosystems have bioengineered the planet in mid-Palaeozoic times? Palaeontology. 58, 803-837
d.o.i: 10.1111/pala.12187

Espada, M., Silva, A. C., Eves van den Akker, S., Cock, P. J., Mota, M. and Jones, J. T. (2015) Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy. Mol Plant Pathold.o.i: 10.1111/mpp.12280
PMC: 25981957

Eves-van den Akker, S., Lilley, C. J., Reid, A., Pickup, J., Anderson, E., Cock, P. J., Blaxter, M., Urwin, P. E., Jones, J. T. and Blok, V. C. (2015) A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual. Mol Ecol. 24, 5842-5851
d.o.i: 10.1111/mec.13434
PMC: 26607216

Flynn, K. J., St John, M., Raven, J. A., Skibinski, D. O. F., Allen, J. I., Mitra, A. and Hofmann, E. E. (2015) Acclimation, adaptation, traits and trade-offs in plankton functional type models: reconciling terminology for biology and modelling. J Plankton Res. 37, 683-691
d.o.i: 10.1093/plankt/fbv036

Forgan, D. H., Mead, A., Cockell, C. S. and Raven, J. A. (2015) Surface flux patterns on planets in circumbinary systems and potential for photosynthesis. Int J Astrobiol. 14, 465-478
d.o.i: 10.1017/S147355041400041x

Fray, R. G. and Simpson, G. G. (2015) The Arabidopsis epitranscriptome. Curr Opin Plant Biol. 27, 17-21
d.o.i: 10.1016/j.pbi.2015.05.015
PMC: 26048078

Fry, W. E., Birch, P. R., Judelson, H. S., Grunwald, N. J., Danies, G., Everts, K. L., Gevens, A. J., Gugino, B. K., Johnson, D. A., Johnson, S. B., McGrath, M. T., Myers, K. L., Ristaino, J. B., Roberts, P. D., Secor, G. and Smart, C. D. (2015) Five Reasons to Consider Phytophthora infestans a Reemerging Pathogen. Phytopathology. 105, 966-981
d.o.i: 10.1094/PHYTO-01-15-0005-FI
PMC: 25760519

Gierlinski, M., Cole, C., Schofield, P., Schurch, N. J., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G., Owen-Hughes, T., Blaxter, M. and Barton, G. J. (2015) Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment. Bioinformatics. 31, 3625-3630
d.o.i: 10.1093/bioinformatics/btv425
PMC: 26206307

Giordano, M., Palmucci, M. and Raven, J. A. (2015) Growth rate hypothesis and efficiency of protein synthesis under different sulphate concentrations in two green algae. Plant Cell and Environment. 38, 2313-2317
d.o.i: 10.1111/pce.12551

He, Q., McLellan, H., Boevink, P. C., Sadanandom, A., Xie, C., Birch, P. R. and Tian, Z. (2015) U-box E3 ubiquitin ligase PUB17 acts in the nucleus to promote specific immune pathways triggered by Phytophthora infestans. J Exp Bot. 66, 3189-3199
d.o.i: 10.1093/jxb/erv128
Pubmed: 4449539
PMC: 25873665

Hemsley, P. A. (2015) The importance of lipid modified proteins in plants. New Phytol. 205, 476-489
d.o.i: 10.1111/nph.13085
PMC: 25283240

Houston, K., Burton, R. A., Sznajder, B., Rafalski, A. J., Dhugga, K. S., Mather, D. E., Taylor, J., Steffenson, B. J., Waugh, R. and Fincher, G. B. (2015) A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family. PLoS One. 10, e0130890
d.o.i: 10.1371/journal.pone.0130890
Pubmed: 4496100
PMC: 26154104

Hurst, C. H. and Hemsley, P. A. (2015) Current perspective on protein S-acylation in plants: more than just a fatty anchor? J Exp Bot. 66, 1599-1606
d.o.i: 10.1093/jxb/erv053
PMC: 25725093

Jaouannet, M., Morris, J. A., Hedley, P. E. and Bos, J. I. (2015) Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance. PLoS Pathog. 11, e1004918
d.o.i: 10.1371/journal.ppat.1004918
Pubmed: 4439036
PMC: 25993686

Lemaire, B., Dlodlo, O., Chimphango, S., Stirton, C., Schrire, B., Boatwright, J. S., Honnay, O., Smets, E., Sprent, J., James, E. K. and Muasya, A. M. (2015) Symbiotic diversity, specificity and distribution of rhizobia in native legumes of the Core Cape Subregion (South Africa). FEMS Microbiol Ecol. 91, 1-17
d.o.i: 10.1093/femsec/fiu024
PMC: 25764552

Marcotuli, I., Houston, K., Waugh, R., Fincher, G. B., Burton, R. A., Blanco, A. and Gadaleta, A. (2015) Genome Wide Association Mapping for Arabinoxylan Content in a Collection of Tetraploid Wheats. PLoS One. 10, e0132787
d.o.i: 10.1371/journal.pone.0132787
Pubmed: 4503733
PMC: 26176552

Motion, G. B., Amaro, T. M., Kulagina, N. and Huitema, E. (2015) Nuclear processes associated with plant immunity and pathogen susceptibility. Brief Funct Genomics. 14, 243-252
d.o.i: 10.1093/bfgp/elv013
Pubmed: 4513213
PMC: 25846755

Motion, G. B., Howden, A. J., Huitema, E. and Jones, S. (2015) DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool. Nucleic Acids Res. 43, e158
d.o.i: 10.1093/nar/gkv805
PMC: 26304539

Obidiegwu, J. E., Bryan, G. J., Jones, H. G. and Prashar, A. (2015) Coping with drought: stress and adaptive responses in potato and perspectives for improvement. Front Plant Sci. 6, 542
d.o.i: 10.3389/fpls.2015.00542
Pubmed: 4510777
PMC: 26257752

O'Malley-James, J. T., Greaves, J. S., Raven, J. A. and Cockell, C. S. (2015) In Search of Future Earths: Assessing the Possibility of Finding Earth Analogues in the Later Stages of Their Habitable Lifetimes. Astrobiology. 15, 400-411
d.o.i: 10.1089/ast.2014.1229

Phillips, D., Jenkins, G., Macaulay, M., Nibau, C., Wnetrzak, J., Fallding, D., Colas, I., Oakey, H., Waugh, R. and Ramsay, L. (2015) The effect of temperature on the male and female recombination landscape of barley. New Phytol. 208, 421-429
d.o.i: 10.1111/nph.13548
PMC: 26255865

Pourkheirandish, M., Hensel, G., Kilian, B., Senthil, N., Chen, G., Sameri, M., Azhaguvel, P., Sakuma, S., Dhanagond, S., Sharma, R., Mascher, M., Himmelbach, A., Gottwald, S., Nair, S. K., Tagiri, A., Yukuhiro, F., Nagamura, Y., Kanamori, H., Matsumoto, T., Willcox, G., Middleton, C. P., Wicker, T., Walther, A., Waugh, R., Fincher, G. B., Stein, N., Kumlehn, J., Sato, K. and Komatsuda, T. (2015) Evolution of the Grain Dispersal System in Barley. Cell. 162, 527-539
d.o.i: 10.1016/j.cell.2015.07.002
PMC: 2623222

Radford, D., Szabo, M., Raven, J. and Ralph, P. J. (2015) Satisfying the Nutrient Tank of Nannochloropsis Oculata; Co-Limitation Reduces Filling Efficiency. Eur J Phycol. 50, 138-139

Raven, J. A. (2015) Implications of mutation of organelle genomes for organelle function and evolution. Journal of Experimental Botany. 66, 5639-5650
d.o.i: 10.1093/jxb/erv298

Raven, J. A. (2015) Harry Smith, FRS: co-founding editor and first Chief Editor of Plant, Cell & Environment. Plant Cell and Environment. 38, 1453-1454
d.o.i: 10.1111/pce.12567

Raven, J. A. (2015) Compartmentation of Defensive Compound Synthesis in a Red Alga. J Phycol. 51, 222-224
d.o.i: 10.1111/jpy.12287

Raven, J. A. (2015) Interactions between Nitrogen and Phosphorus Metabolism. Annu Plant Rev. 48, 187-214
d.o.i: 10.1002/9781118958841.ch7

Raven, J. A. and Beardall, J. (2015) The ins and outs of CO2. J Exp Botd.o.i: 10.1093/jxb/erv451
PMC: 26466660

Raven, J. A. and Griffiths, H. (2015) Photosynthesis in reproductive structures: costs and benefits. Journal of Experimental Botany. 66, 1699-1705
d.o.i: 10.1093/jxb/erv009
PMC: WOS:000353894100001

Raven, J. A. and Ralph, P. J. (2015) Enhanced biofuel production using optimality, pathway modification and waste minimization. J Appl Phycol. 27, 1-31
d.o.i: 10.1007/s10811-014-0323-5
PMC: WOS:000348137600001

Ribeiro, A., Golicz, A., Hackett, C. A., Milne, I., Stephen, G., Marshall, D., Flavell, A. J. and Bayer, M. (2015) An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome. BMC Bioinformatics. 16, 382
d.o.i: 10.1186/s12859-015-0801-z
Pubmed: 4642669
PMC: 26558718

Schlaen, R. G., Mancini, E., Sanchez, S. E., Perez-Santangelo, S., Rugnone, M. L., Simpson, C. G., Brown, J. W., Zhang, X., Chernomoretz, A. and Yanovsky, M. J. (2015) The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms. Proc Natl Acad Sci U S A. 112, 9382-9387
d.o.i: 10.1073/pnas.1504541112
Pubmed: 4522771
PMC: 26170331

Schwerdt, J. G., MacKenzie, K., Wright, F., Oehme, D., Wagner, J. M., Harvey, A. J., Shirley, N. J., Burton, R. A., Schreiber, M., Halpin, C., Zimmer, J., Marshall, D. F., Waugh, R. and Fincher, G. B. (2015) Evolutionary Dynamics of the Cellulose Synthase Gene Superfamily in Grasses. Plant Physiol. 168, 968-983
d.o.i: 10.1104/pp.15.00140
PMC: 25999407

Staiger, D. and Simpson, G. G. (2015) Enter exitrons. Genome Biol. 16, 136
d.o.i: 10.1186/s13059-015-0704-3
Pubmed: 4494720
PMC: 26149172

Tamburic, B., Evenhuis, C. R., Suggett, D. J., Larkum, A. W., Raven, J. A. and Ralph, P. J. (2015) Gas Transfer Controls Carbon Limitation During Biomass Production by Marine Microalgae. ChemSusChem. 8, 2727-2736
d.o.i: 10.1002/cssc.201500332
PMC: 26212226

Tamburic, B., Evenhuis, C. R., Suggett, D. J., Larkum, A. W. D., Raven, J. A. and Ralph, P. J. (2015) Gas Transfer Controls Carbon Limitation During Biomass Production by Marine Microalgae. Chemsuschem. 8, 2727-2736
d.o.i: 10.1002/cssc.201500332

Tavakol, E., Okagaki, R., Verderio, G., Shariati, J. V., Hussien, A., Bilgic, H., Scanlon, M. J., Todt, N. R., Close, T. J., Druka, A., Waugh, R., Steuernagel, B., Ariyadasa, R., Himmelbach, A., Stein, N., Muehlbauer, G. J. and Rossini, L. (2015) The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning. Plant Physiol. 168, 164-174
d.o.i: 10.1104/pp.114.252882
Pubmed: 4424007
PMC: 25818702

Vieira, P., Eves-van den Akker, S., Verma, R., Wantoch, S., Eisenback, J. D. and Kamo, K. (2015) The Pratylenchus penetrans Transcriptome as a Source for the Development of Alternative Control Strategies: Mining for Putative Genes Involved in Parasitism and Evaluation of in planta RNAi. PLoS One. 10, e0144674
d.o.i: 10.1371/journal.pone.0144674
PMC: 26658731

Wang, X., Boevink, P., McLellan, H., Armstrong, M., Bukharova, T., Qin, Z. and Birch, P. R. (2015) A Host KH RNA-Binding Protein Is a Susceptibility Factor Targeted by an RXLR Effector to Promote Late Blight Disease. Mol Plant. 8, 1385-1395
d.o.i: 10.1016/j.molp.2015.04.012
Pubmed: 4560694
PMC: 25936676

Wiesel, L., Davis, J. L., Milne, L., Redondo Fernandez, V., Herold, M. B., Middlefell Williams, J., Morris, J., Hedley, P. E., Harrower, B., Newton, A. C., Birch, P. R., Gilroy, E. M. and Hein, I. (2015) A transcriptional reference map of defence hormone responses in potato. Sci Rep. 5, 15229
d.o.i: 10.1038/srep15229
Pubmed: 4610000
PMC: 26477733

Zhang, R., Calixto, C. P., Tzioutziou, N. A., James, A. B., Simpson, C. G., Guo, W., Marquez, Y., Kalyna, M., Patro, R., Eyras, E., Barta, A., Nimmo, H. G. and Brown, J. W. (2015) AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana. New Phytol. 208, 96-101
d.o.i: 10.1111/nph.13545
PMC: 26111100