University of Dundee

Plant Sciences 2016

Adams, M.A., Turnbull, T.L., Sprent, J.I., and Buchmann, N. (2016) Legumes are different: Leaf nitrogen, photosynthesis, and water use efficiency. Proceedings of the National Academy of Sciences of the United States of America. d.o.i 10.1073/pnas.1523936113
Pubmed 4839396
PMC 27035971

Alegria Terrazas, R., Giles, C., Paterson, E., Robertson-Albertyn, S., Cesco, S., Mimmo, T., Pii, Y., and Bulgarelli, D. (2016) Plant-Microbiota Interactions as a Driver of the Mineral Turnover in the Rhizosphere. Advances in applied microbiology. 95, 1-67
d.o.i 10.1016/bs.aambs.2016.03.001
PMC 27261781

Andriotis, V.M., Saalbach, G., Waugh, R., Field, R.A., and Smith, A.M. (2016) The Maltase Involved in Starch Metabolism in Barley Endosperm Is Encoded by a Single Gene. PloS one. 11, e0151642
d.o.i 10.1371/journal.pone.0151642
Pubmed 4807107
PMC 27011041

Boevink, P.C., McLellan, H., Gilroy, E.M., Naqvi, S., He, Q., Yang, L., Wang, X., Turnbull, D., Armstrong, M.R., Tian, Z., and Birch, P.R. (2016) Oomycetes Seek Help from the Plant: Phytophthora infestans Effectors Target Host Susceptibility Factors. Molecular plant. 9, 636-638
d.o.i 10.1016/j.molp.2016.04.005
PMC 27095376

Boevink, P.C., Wang, X., McLellan, H., He, Q., Naqvi, S., Armstrong, M.R., Zhang, W., Hein, I., Gilroy, E.M., Tian, Z., and Birch, P.R. (2016) A Phytophthora infestans RXLR effector targets plant PP1c isoforms that promote late blight disease. Nature communications. 7, 10311
d.o.i 10.1038/ncomms10311
Pubmed 4740116
PMC 26822079

Bontemps, C., Rogel, M.A., Wiechmann, A., Mussabekova, A., Moody, S., Simon, M.F., Moulin, L., Elliott, G.N., Lacercat-Didier, L., Dasilva, C., Grether, R., Camargo-Ricalde, S.L., Chen, W., Sprent, J.I., Martinez-Romero, E., Young, J.P., and James, E.K. (2016) Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts. The New phytologist. 209, 319-333
d.o.i 10.1111/nph.13573
PMC 26214613

Brown, J.W., Calixto, C.P., and Zhang, R. (2016) High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants. The New phytologist. d.o.i 10.1111/nph.14208
PMC 27659901

Calixto, C.P., Simpson, C.G., Waugh, R., and Brown, J.W. (2016) Alternative Splicing of Barley Clock Genes in Response to Low Temperature. PloS one. 11, e0168028
d.o.i 10.1371/journal.pone.0168028
PMC 27959947

Carvalho, R.F., Szakonyi, D., Simpson, C.G., Barbosa, I.C., Brown, J.W., Baena-Gonzalez, E., and Duque, P. (2016) The Arabidopsis SR45 Splicing Factor, a Negative Regulator of Sugar Signaling, Modulates SNF1-Related Protein Kinase 1 Stability. The Plant cell. 28, 1910-1925
d.o.i 10.1105/tpc.16.00301
Pubmed 5006706
PMC 27436712

Colas, I., Macaulay, M., Higgins, J.D., Phillips, D., Barakate, A., Posch, M., Armstrong, S.J., Franklin, F.C., Halpin, C., Waugh, R., and Ramsay, L. (2016) A spontaneous mutation in MutL-Homolog 3 (HvMLH3) affects synapsis and crossover resolution in the barley desynaptic mutant des10. The New phytologist. 212, 693-707
d.o.i 10.1111/nph.14061
PMC 27392293

Eves-van den Akker, S., and Birch, P.R. (2016) Opening the Effector Protein Toolbox for Plant-Parasitic Cyst Nematode Interactions. Molecular plant. 9, 1451-1453
d.o.i 10.1016/j.molp.2016.09.008
Pubmed 5106285
PMC 27693399

Eves-van den Akker, S., Laetsch, D.R., Thorpe, P., Lilley, C.J., Danchin, E.G.J., Da Rocha, M., Rancurel, C., Holroyd, N.E., Cotton, J.A., Szitenberg, A., Grenier, E., Montarry, J., Mimee, B., Duceppe, M.O., Boyes, I., Marvin, J.M.C., Jones, L.M., Yusup, H.B., Lafond-Lapalme, J., Esquibet, M., Sabeh, M., Rott, M., Overmars, H., Finkers-Tomczak, A., Smant, G., Koutsovoulos, G., Blok, V., Mantelin, S., Cock, P.J.A., Phillips, W., Henrissat, B., Urwin, P.E., Blaxter, M., and Jones, J.T. (2016) The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology. 17, d.o.i Artn 124
10.1186/S13059-016-0985-1
PMC WOS:000378899700001

Eves-Van den Akker, S., Lilley, C.J., Yusup, H.B., Jones, J.T., and Urwin, P.E. (2016) Functional C-TERMINALLY ENCODED PEPTIDE (CEP) plant hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis. Molecular plant pathology. 17, 1265-1275
d.o.i 10.1111/mpp.12402
PMC WOS:000383680800010

Jost, M., Hensel, G., Kappel, C., Druka, A., Sicard, A., Hohmann, U., Beier, S., Himmelbach, A., Waugh, R., Kumlehn, J., Stein, N., and Lenhard, M. (2016) The INDETERMINATE DOMAIN Protein BROAD LEAF1 Limits Barley Leaf Width by Restricting Lateral Proliferation. Current biology : CB. 26, 903-909
d.o.i 10.1016/j.cub.2016.01.047
PMC 26996502

Jost, M., Taketa, S., Mascher, M., Himmelbach, A., Yuo, T., Shahinnia, F., Rutten, T., Druka, A., Schmutzer, T., Steuernagel, B., Beier, S., Taudien, S., Scholz, U., Morgante, M., Waugh, R., and Stein, N. (2016) A Homolog of Blade-On-Petiole 1 and 2 (BOP1/2) Controls Internode Length and Homeotic Changes of the Barley Inflorescence. Plant physiology. 171, 1113-1127
d.o.i 10.1104/pp.16.00124
Pubmed 4902598
PMC 27208226

Kumar, M., Wightman, R., Atanassov, I., Gupta, A., Hurst, C.H., Hemsley, P.A., and Turner, S. (2016) S-Acylation of the cellulose synthase complex is essential for its plasma membrane localization. Science. 353, 166-169
d.o.i 10.1126/science.aaf4009
PMC 27387950

Kwenda, S., Birch, P.R., and Moleleki, L.N. (2016) Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection. BMC genomics. 17, 614
d.o.i 10.1186/s12864-016-2967-9
Pubmed 4982125
PMC 27515663

Kwenda, S., Gorshkov, V., Ramesh, A.M., Naidoo, S., Rubagotti, E., Birch, P.R., and Moleleki, L.N. (2016) Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum. BMC genomics. 17, 47
d.o.i 10.1186/s12864-016-2376-0
Pubmed 4710047
PMC 26753530

Lavoie, M., Raven, J.A., and Levasseur, M. (2016) Energy cost and putative benefits of cellular mechanisms modulating buoyancy in aflagellate marine phytoplankton. Journal of phycology. 52, 239-251
d.o.i 10.1111/jpy.12390
PMC 27037589

Marcotuli, I., Houston, K., Schwerdt, J.G., Waugh, R., Fincher, G.B., Burton, R.A., Blanco, A., and Gadaleta, A. (2016) Genetic Diversity and Genome Wide Association Study of beta-Glucan Content in Tetraploid Wheat Grains. PloS one. 11, e0152590
d.o.i 10.1371/journal.pone.0152590
Pubmed 4821454
PMC 27045166

Mascher, M., Schuenemann, V.J., Davidovich, U., Marom, N., Himmelbach, A., Hubner, S., Korol, A., David, M., Reiter, E., Riehl, S., Schreiber, M., Vohr, S.H., Green, R.E., Dawson, I.K., Russell, J., Kilian, B., Muehlbauer, G.J., Waugh, R., Fahima, T., Krause, J., Weiss, E., and Stein, N. (2016) Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nature genetics. 48, 1089-1093
d.o.i 10.1038/ng.3611
PMC 27428749

Mitra, A., Flynn, K.J., Tillmann, U., Raven, J.A., Caron, D., Stoecker, D.K., Not, F., Hansen, P.J., Hallegraeff, G., Sanders, R., Wilken, S., McManus, G., Johnson, M., Pitta, P., Vage, S., Berge, T., Calbet, A., Thingstad, F., Jeong, H.J., Burkholder, J., Glibert, P.M., Graneli, E., and Lundgren, V. (2016) Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition: Incorporation of Diverse Mixotrophic Strategies. Protist. 167, 106-120
d.o.i 10.1016/j.protis.2016.01.003
PMC 26927496

Mora, F., Quitral, Y.A., Matus, I., Russell, J., Waugh, R., and Del Pozo, A. (2016) SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach. Frontiers in plant science. 7, 909
d.o.i 10.3389/fpls.2016.00909
Pubmed 4921488
PMC 27446139

Noon, J.B., Qi, M.S., Sill, D.N., Muppirala, U., Eves-van den Akker, S., Maier, T.R., Dobbs, D., Mitchum, M.G., Hewezi, T., and Baum, T.J. (2016) A Plasmodium-like virulence effector of the soybean cyst nematode suppresses plant innate immunity. New Phytologist. 212, 444-460
d.o.i 10.1111/nph.14047
PMC WOS:000383595700019

Oakey, H., Cullis, B., Thompson, R., Comadran, J., Halpin, C., and Waugh, R. (2016) Genomic Selection in Multi-environment Crop Trials. G3. 6, 1313-1326
d.o.i 10.1534/g3.116.027524
Pubmed 4856083
PMC 26976443

Prashar, A., and Jones, H.G. (2016) Assessing Drought Responses Using Thermal Infrared Imaging. Methods in molecular biology. 1398, 209-219
d.o.i 10.1007/978-1-4939-3356-3_17
PMC 26867626

Raven, J.A., and Beardall, J. (2016) The ins and outs of CO2. Journal of experimental botany. 67, 1-13
d.o.i 10.1093/jxb/erv451
Pubmed 4682431
PMC 26466660

Raven, J.A., and Colmer, T.D. (2016) Life at the boundary: photosynthesis at the soil-fluid interface. A synthesis focusing on mosses. Journal of experimental botany. 67, 1613-1623
d.o.i 10.1093/jxb/erw012
PMC 26842980

Russell, J., Mascher, M., Dawson, I.K., Kyriakidis, S., Calixto, C., Freund, F., Bayer, M., Milne, I., Marshall-Griffiths, T., Heinen, S., Hofstad, A., Sharma, R., Himmelbach, A., Knauft, M., van Zonneveld, M., Brown, J.W., Schmid, K., Kilian, B., Muehlbauer, G.J., Stein, N., and Waugh, R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nature genetics. 48, 1024-1030
d.o.i 10.1038/ng.3612
PMC 27428750

Schurch, N.J., Schofield, P., Gierlinski, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G.G., Owen-Hughes, T., Blaxter, M., and Barton, G.J. (2016) How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? Rna. 22, 839-851
d.o.i 10.1261/rna.053959.115
Pubmed 4878611
PMC 27022035

Simpson, C.G., Fuller, J., Calixto, C.P., McNicol, J., Booth, C., Brown, J.W., and Staiger, D. (2016) Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes. Methods in molecular biology. 1398, 119-132
d.o.i 10.1007/978-1-4939-3356-3_11
PMC 26867620

Stocker, B.D., Prentice, I.C., Cornell, S.E., Davies-Barnard, T., Finzi, A.C., Franklin, O., Janssens, I., Larmola, T., Manzoni, S., Nasholm, T., Raven, J.A., Rebel, K.T., Reed, S., Vicca, S., Wiltshire, A., and Zaehle, S. (2016) Terrestrial nitrogen cycling in Earth system models revisited. The New phytologist. 210, 1165-1168
d.o.i 10.1111/nph.13997
PMC 27159524

Thorpe, P., Cock, P.J., and Bos, J. (2016) Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets. BMC genomics. 17, 172
d.o.i 10.1186/s12864-016-2496-6
Pubmed 4776380
PMC 26935069

Van Weymers, P.S., Baker, K., Chen, X., Harrower, B., Cooke, D.E., Gilroy, E.M., Birch, P.R., Thilliez, G.J., Lees, A.K., Lynott, J.S., Armstrong, M.R., McKenzie, G., Bryan, G.J., and Hein, I. (2016) Utilizing "Omic" Technologies to Identify and Prioritize Novel Sources of Resistance to the Oomycete Pathogen Phytophthora infestans in Potato Germplasm Collections. Frontiers in plant science. 7, 672
d.o.i 10.3389/fpls.2016.00672
Pubmed 4882398
PMC 27303410

Whisson, S.C., Boevink, P.C., Wang, S., and Birch, P.R. (2016) The cell biology of late blight disease. Current opinion in microbiology. 34, 127-135
d.o.i 10.1016/j.mib.2016.09.002
PMC 27723513

Yang, L., McLellan, H., Naqvi, S., He, Q., Boevink, P.C., Armstrong, M., Giuliani, L.M., Zhang, W., Tian, Z., Zhan, J., Gilroy, E.M., and Birch, P.R. (2016) Potato NPH3/RPT2-Like Protein StNRL1, Targeted by a Phytophthora infestans RXLR Effector, Is a Susceptibility Factor. Plant physiology. 171, 645-657
d.o.i 10.1104/pp.16.00178
Pubmed 4854710
PMC 26966171

Zhang, R., Tucker, M.R., Burton, R.A., Shirley, N.J., Little, A., Morris, J., Milne, L., Houston, K., Hedley, P.E., Waugh, R., and Fincher, G.B. (2016) The Dynamics of Transcript Abundance during Cellularization of Developing Barley Endosperm. Plant physiology. 170, 1549-1565
d.o.i 10.1104/pp.15.01690
Pubmed 4775131
PMC 26754666

Zhang, Y., Rataj, K., Simpson, G.G., and Tong, L. (2016) Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA. PloS one. 11, e0160694
d.o.i 10.1371/journal.pone.0160694
Pubmed 4981400
PMC 27513867