University of Dundee

Plant Sciences 2017

Amaro, T., Thilliez, G.J.A., McLeod, R.A., and Huitema, E. (2017) Random mutagenesis screen shows that Phytophthora capsici CRN83_152-mediated cell death is not required for its virulence function(s). Molecular plant pathology.

 d.o.i 10.1111/mpp.12590

PMC 28779542

Amaro, T.M., Thilliez, G.J., Motion, G.B., and Huitema, E. (2017) A Perspective on CRN Proteins in the Genomics Age: Evolution, Classification, Delivery and Function Revisited. Frontiers in plant science. 8, 99

d.o.i 10.3389/fpls.2017.00099

Pubmed 5289972

PMC 28217133

Bayer, M.M., Rapazote-Flores, P., Ganal, M., Hedley, P.E., Macaulay, M., Plieske, J., Ramsay, L., Russell, J., Shaw, P.D., Thomas, W., and Waugh, R. (2017) Development and Evaluation of a Barley 50k iSelect SNP Array. Frontiers in plant science. 8, 1792

d.o.i 10.3389/fpls.2017.01792

Pubmed 5651081

PMC 29089957

Beardall, J., and Raven, J.A. (2017) Cyanobacteria vs green algae: which group has the edge? Journal of experimental botany. 68, 3697-3699

d.o.i 10.1093/jxb/erx226

PMC 28911057

Beier, S., Himmelbach, A., Colmsee, C., Zhang, X.Q., Barrero, R.A., Zhang, Q., Li, L., Bayer, M., Bolser, D., Taudien, S., Groth, M., Felder, M., Hastie, A., Simkova, H., Stankova, H., Vrana, J., Chan, S., Munoz-Amatriain, M., Ounit, R., Wanamaker, S., Schmutzer, T., Aliyeva-Schnorr, L., Grasso, S., Tanskanen, J., Sampath, D., Heavens, D., Cao, S., Chapman, B., Dai, F., Han, Y., Li, H., Li, X., Lin, C., McCooke, J.K., Tan, C., Wang, S., Yin, S., Zhou, G., Poland, J.A., Bellgard, M.I., Houben, A., Dolezel, J., Ayling, S., Lonardi, S., Langridge, P., Muehlbauer, G.J., Kersey, P., Clark, M.D., Caccamo, M., Schulman, A.H., Platzer, M., Close, T.J., Hansson, M., Zhang, G., Braumann, I., Li, C., Waugh, R., Scholz, U., Stein, N., and Mascher, M. (2017) Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Scientific data. 4, 170044

d.o.i 10.1038/sdata.2017.44

Pubmed 5407242

PMC 28448065

Bellucci, A., Tondelli, A., Fangel, J.U., Torp, A.M., Xu, X., Willats, W.G., Flavell, A., Cattivelli, L., and Rasmussen, S.K. (2017) Genome-wide association mapping in winter barley for grain yield and culm cell wall polymer content using the high-throughput CoMPP technique. PloS one. 12, e0173313

d.o.i 10.1371/journal.pone.0173313

Pubmed 5354286

PMC 28301509

Brodie, J., Ball, S.G., Bouget, F.Y., Chan, C.X., De Clerck, O., Cock, J.M., Gachon, C., Grossman, A.R., Mock, T., Raven, J.A., Saha, M., Smith, A.G., Vardi, A., Yoon, H.S., and Bhattacharya, D. (2017) Biotic interactions as drivers of algal origin and evolution. The New phytologist. 216, 670-681

d.o.i 10.1111/nph.14760

PMC 28857164

Brodie, J., Chan, C.X., De Clerck, O., Cock, J.M., Coelho, S.M., Gachon, C., Grossman, A.R., Mock, T., Raven, J.A., Smith, A.G., Yoon, H.S., and Bhattacharya, D. (2017) The Algal Revolution. Trends in plant science. 22, 726-738

d.o.i 10.1016/j.tplants.2017.05.005

PMC 28610890

Brown, J.W., Calixto, C.P., and Zhang, R. (2017) High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants. The New phytologist. 213, 525-530

d.o.i 10.1111/nph.14208

PMC 27659901

 Brown, J.W.L., Pardini, M., Brownlee, W.J., Fernando, K., Samson, R.S., Carrasco, F.P., Ourselin, S., Wheeler-Kingshott, C.A.M.G., Miller, D.H., and Chard, D.T. (2017) An abnormal periventricular magnetization transfer ratio gradient occurs early in multiple sclerosis. Brain. 140, 387-398

d.o.i 10.1093/brain/aww296

PMC WOS:000397315900022

 Bryan, G.J., McLean, K., Waugh, R., and Spooner, D.M. (2017) Levels of Intra-specific AFLP Diversity in Tuber-Bearing Potato Species with Different Breeding Systems and Ploidy Levels. Frontiers in genetics. 8, 119

d.o.i 10.3389/fgene.2017.00119

Pubmed 5613152

PMC 28983315

 Bull, H., Casao, M.C., Zwirek, M., Flavell, A.J., Thomas, W.T.B., Guo, W., Zhang, R., Rapazote-Flores, P., Kyriakidis, S., Russell, J., Druka, A., McKim, S.M., and Waugh, R. (2017) Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility. Nature communications. 8, 936

d.o.i 10.1038/s41467-017-00940-7

Pubmed 5643332

PMC 29038434

Colas, I., Darrier, B., Arrieta, M., Mittmann, S.U., Ramsay, L., Sourdille, P., and Waugh, R. (2017) Observation of Extensive Chromosome Axis Remodeling during the "Diffuse-Phase" of Meiosis in Large Genome Cereals. Frontiers in plant science. 8, 1235

d.o.i 10.3389/fpls.2017.01235

Pubmed 5508023

PMC 28751906

Cornwall, C.E., Revill, A.T., Hall-Spencer, J.M., Milazzo, M., Raven, J.A., and Hurd, C.L. (2017) Inorganic carbon physiology underpins macroalgal responses to elevated CO2. Scientific reports. 7, 46297

d.o.i 10.1038/srep46297

Pubmed 5394685

PMC 28417970

Cummins, M., and Huitema, E. (2017) Effector-Decoy Pairs: Another Countermeasure Emerging during Host-Microbe Co-evolutionary Arms Races? Molecular plant. 10, 662-664

d.o.i 10.1016/j.molp.2017.03.008

PMC 28365332

Danchin, E.G.J., Perfus-Barbeoch, L., Rancurel, C., Thorpe, P., Da Rocha, M., Bajew, S., Neilson, R., Guzeeva, E.S., Da Silva, C., Guy, J., Labadie, K., Esmenjaud, D., Helder, J., Jones, J.T., and den Akker, S.E. (2017) The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes. Genes. 8, d.o.i 10.3390/genes8100287

Pubmed 5664137

PMC 29065523

Escudero, C., Morris, J.A., Hedley, P.E., and Bos, J.I.B. (2017) Barley transcriptome analyses upon interaction with different aphid species identifies thionins contributing to resistance. Plant, cell & environment.

d.o.i 10.1111/pce.12979

PMC 28452058

 Franco-Orozco, B., Berepiki, A., Ruiz, O., Gamble, L., Griffe, L.L., Wang, S., Birch, P.R.J., Kanyuka, K., and Avrova, A. (2017) A new proteinaceous pathogen-associated molecular pattern (PAMP) identified in Ascomycete fungi induces cell death in Solanaceae. The New phytologist. 214, 1657-1672

d.o.i 10.1111/nph.14542

PMC 28386988

 Guo, W., Calixto, C.P.G., Brown, J.W.S., and Zhang, R. (2017) TSIS: an R package to infer alternative splicing isoform switches for time-series data. Bioinformatics. 33, 3308-3310

d.o.i 10.1093/bioinformatics/btx411

PMC 29028262

 Guo, W., Calixto, C.P.G., Tzioutziou, N., Lin, P., Waugh, R., Brown, J.W.S., and Zhang, R. (2017) Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size. BMC systems biology. 11, 62

d.o.i 10.1186/s12918-017-0440-2

Pubmed 5477119

PMC 28629365

Hassan, A.S., Houston, K., Lahnstein, J., Shirley, N., Schwerdt, J.G., Gidley, M.J., Waugh, R., Little, A., and Burton, R.A. (2017) A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain. PloS one. 12, e0182537

d.o.i 10.1371/journal.pone.0182537

Pubmed 5542645

PMC 28771585

Hemsley, P.A. (2017) An outlook on protein S-acylation in plants: what are the next steps? Journal of experimental botany. d.o.i 10.1093/jxb/erw497

Pubmed PMC 28158736

Howden, A.J.M., Stam, R., Martinez Heredia, V., Motion, G.B., Ten Have, S., Hodge, K., Marques Monteiro Amaro, T.M., and Huitema, E. (2017) Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity. The New phytologist. 215, 309-322

d.o.i 10.1111/nph.14540

PMC 28394025

 Hughes, J., Hepworth, C., Dutton, C., Dunn, J.A., Hunt, L., Stephens, J., Waugh, R., Cameron, D.D., and Gray, J.E. (2017) Reducing Stomatal Density in Barley Improves Drought Tolerance without Impacting on Yield. Plant physiology. 174, 776-787

d.o.i 10.1104/pp.16.01844

PMC 28461401

Hurst, C.H., Turnbull, D., Plain, F., Fuller, W., and Hemsley, P.A. (2017) Maleimide scavenging enhances determination of protein S-palmitoylation state in acyl-exchange methods. BioTechniques. 62, 69-75

d.o.i 10.2144/000114516

Pubmed 5400063

PMC 28193150

 Hurst, C.H., Turnbull, D., Plain, F., Fuller, W., and Hemsley, P.A. (2017) Maleimide scavenging enhances determination of protein S-palmitoylation state in acyl-exchange methods. BioTechniques. 62, 69-75

d.o.i 10.2144/000114516

Pubmed 5400063

PMC 28193150

 Kikuchi, T., Eves-van den Akker, S., and Jones, J.T. (2017) Genome Evolution of Plant-Parasitic Nematodes. Annual review of phytopathology. 55, 333-354

d.o.i 10.1146/annurev-phyto-080516-035434

 PMC 28590877

 Kim, M., Brodersen, K.E., Szabo, M., Larkum, A.W.D., Raven, J.A., Ralph, P.J., and Pernice, M. (2017) Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass Zostera muelleri. Photosynthesis research.

d.o.i 10.1007/s11120-017-0452-1

PMC 28980125

Larkum, A.W.D., Davey, P.A., Kuo, J., Ralph, P.J., and Raven, J.A. (2017) Carbon-concentrating mechanisms in seagrasses. Journal of experimental botany. 68, 3773-3784

d.o.i 10.1093/jxb/erx206

PMC 28911056

Leles, S.G., Mitra, A., Flynn, K.J., Stoecker, D.K., Hansen, P.J., Calbet, A., McManus, G.B., Sanders, R.W., Caron, D.A., Not, F., Hallegraeff, G.M., Pitta, P., Raven, J.A., Johnson, M.D., Glibert, P.M., and Vage, S. (2017) Oceanic protists with different forms of acquired phototrophy display contrasting biogeographies and abundance. Proceedings. Biological sciences. 284,

d.o.i 10.1098/rspb.2017.0664

Pubmed 5563798

PMC 28768886

Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S.O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P.E., Russell, J., Bayer, M., Ramsay, L., Liu, H., Haberer, G., Zhang, X.Q., Zhang, Q., Barrero, R.A., Li, L., Taudien, S., Groth, M., Felder, M., Hastie, A., Simkova, H., Stankova, H., Vrana, J., Chan, S., Munoz-Amatriain, M., Ounit, R., Wanamaker, S., Bolser, D., Colmsee, C., Schmutzer, T., Aliyeva-Schnorr, L., Grasso, S., Tanskanen, J., Chailyan, A., Sampath, D., Heavens, D., Clissold, L., Cao, S., Chapman, B., Dai, F., Han, Y., Li, H., Li, X., Lin, C., McCooke, J.K., Tan, C., Wang, P., Wang, S., Yin, S., Zhou, G., Poland, J.A., Bellgard, M.I., Borisjuk, L., Houben, A., Dolezel, J., Ayling, S., Lonardi, S., Kersey, P., Langridge, P., Muehlbauer, G.J., Clark, M.D., Caccamo, M., Schulman, A.H., Mayer, K.F.X., Platzer, M., Close, T.J., Scholz, U., Hansson, M., Zhang, G., Braumann, I., Spannagl, M., Li, C., Waugh, R., and Stein, N. (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature. 544, 427-433

d.o.i 10.1038/nature22043

PMC 28447635

Mckim, S.M., Routier-Kierzkowska, A.L., Monniaux, M., Kierzkowski, D., Pieper, B., Smith, R.S., Tsiantis, M., and Hay, A. (2017) Seasonal Regulation of Petal Number. Plant physiology. 175, 886-903

d.o.i 10.1104/pp.17.00563

PMC WOS:000411813400024

Michelmore, R., Coaker, G., Bart, R., Beattie, G., Bent, A., Bruce, T., Cameron, D., Dangl, J., Dinesh-Kumar, S., Edwards, R., Eves-van den Akker, S., Gassmann, W., Greenberg, J.T., Hanley-Bowdoin, L., Harrison, R.J., Harvey, J., He, P., Huffaker, A., Hulbert, S., Innes, R., Jones, J.D.G., Kaloshian, I., Kamoun, S., Katagiri, F., Leach, J., Ma, W., McDowell, J., Medford, J., Meyers, B., Nelson, R., Oliver, R., Qi, Y., Saunders, D., Shaw, M., Smart, C., Subudhi, P., Torrance, L., Tyler, B., Valent, B., and Walsh, J. (2017) Foundational and Translational Research Opportunities to Improve Plant Health. Molecular plant-microbe interactions : MPMI. 30, 515-516

d.o.i 10.1094/MPMI-01-17-0010-CR

PMC 28398839

Monniaux, M., McKim, S.M., Cartolano, M., Thevenon, E., Parcy, F., Tsiantis, M., and Hay, A. (2017) Conservation vs divergence in LEAFY and APETALA1 functions between Arabidopsis thaliana and Cardamine hirsuta. New Phytologist. 216, 549-561

d.o.i 10.1111/nph.14419

PMC WOS:000410964800022

Orosa, B., He, Q., Mesmar, J., Gilroy, E.M., McLellan, H., Yang, C., Craig, A., Bailey, M., Zhang, C., Moore, J.D., Boevink, P.C., Tian, Z., Birch, P.R., and Sadanandom, A. (2017) BTB-BACK Domain Protein POB1 Suppresses Immune Cell Death by Targeting Ubiquitin E3 ligase PUB17 for Degradation. PLoS genetics. 13, e1006540

d.o.i 10.1371/journal.pgen.1006540

Pubmed 5249250

PMC 28056034

Phillips, W.S., Eves-van den Akker, S., and Zasada, I.A. (2017) Draft Transcriptome of Globodera ellingtonae. J Nematol. 49, 129-130

Pubmed 5507131

PMC 28706310

Phillips, W.S., Howe, D.K., Brown, A.M.V., Eves-van den Akker, S., Dettwyler, L., Peetz, A.B., Denver, D.R., and Zasada, I.A. (2017) The Draft Genome of Globodera ellingtonae. J Nematol. 49, 127-128

Pubmed 5507130

PMC 28706309

Pierangelini, M., Raven, J.A., and Giordano, M. (2017) The relative availability of inorganic carbon and inorganic nitrogen influences the response of the dinoflagellate Protoceratium reticulatum to elevated CO2. Journal of phycology. 53, 298-307

d.o.i 10.1111/jpy.12463

PMC 27624862

Prade, V.M., Gundlach, H., Twardziok, S., Chapman, B., Tan, C., Langridge, P., Schulman, A.H., Stein, N., Waugh, R., Zhang, G., Platzer, M., Li, C., Spannagl, M., and Mayer, K.F.X. (2017) The Pseudogenes of Barley. The Plant journal : for cell and molecular biology.

d.o.i 10.1111/tpj.13794

PMC 29205595

Rathore, R., Dowling, D.N., Forristal, P.D., Spink, J., Cotter, P.D., Bulgarelli, D., and Germaine, K.J. (2017) Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape (Brassica napus). Frontiers in microbiology. 8, 1489

d.o.i 10.3389/fmicb.2017.01489

Pubmed 5553296

PMC 28848510

 Raven, J.A., Beardall, J., and Sanchez-Baracaldo, P. (2017) The possible evolution, and future, of CO2-concentrating mechanisms. Journal of experimental botany.

d.o.i 10.1093/jxb/erx110

PMC 28505361

 Raven, J.A., and Colmer, T.D. (2017) Corrigendum: Life at the boundary: photosynthesis at the soil-fluid interface. A synthesis focusing on mosses. Journal of experimental botany. 68, 5247

d.o.i 10.1093/jxb/erw308

PMC 27531887

Raven, J.A., and Giordano, M. (2017) Acquisition and metabolism of carbon in the Ochrophyta other than diatoms. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 372,

d.o.i 10.1098/rstb.2016.0400

Pubmed 5516109

PMC 28717026

 Robertson-Albertyn, S., Terrazas, R.A., Balbirnie, K., Blank, M., Janiak, A., Szarejko, I., Chmielewska, B., Karcz, J., Morris, J., Hedley, P.E., George, T.S., and Bulgarelli, D. (2017) Root Hair Mutations Displace the Barley Rhizosphere Microbiota. Frontiers in plant science. 8,

d.o.i Artn 109410.3389/Fpls.2017.01094

PMC WOS:000404008400001

 Rodriguez, P.A., Escudero-Martinez, C., and Bos, J.I.B. (2017) An Aphid Effector Targets Trafficking Protein VPS52 in a Host-Specific Manner to Promote Virulence. Plant physiology. 173, 1892-1903

d.o.i 10.1104/pp.16.01458

PMC WOS:000400366900028

Ruan, Z., Raven, J.A., and Giordano, M. (2017) In Synechococcus sp. competition for energy between assimilation and acquisition of C and those of N only occurs when growth is light limited. Journal of experimental botany.

d.o.i 10.1093/jxb/erx074

PMC 28369501

Sakuma, S., Lundqvist, U., Kakei, Y., Thirulogachandar, V., Suzuki, T., Hori, K., Wu, J., Tagiri, A., Rutten, T., Koppolu, R., Shimada, Y., Houston, K., Thomas, W.T.B., Waugh, R., Schnurbusch, T., and Komatsuda, T. (2017) Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor. Plant physiology. 175, 1720-1731

d.o.i 10.1104/pp.17.01149

Pubmed 5717734

PMC 29101279

Sanchez-Baracaldo, P., Bianchini, G., Huelsenbeck, J.P., Raven, J.A., Pisani, D., and Knoll, A.H. (2017) Reply to Nakov et al.: Model choice requires biological insight when studying the ancestral habitat of photosynthetic eukaryotes. Proceedings of the National Academy of Sciences of the United States of America. 114, E10608-E10609

d.o.i 10.1073/pnas.1717417114

PMC 29208724

Sanchez-Baracaldo, P., Raven, J.A., Pisani, D., and Knoll, A.H. (2017) Early photosynthetic eukaryotes inhabited low-salinity habitats. Proceedings of the National Academy of Sciences of the United States of America. 114, E7737-E7745

d.o.i 10.1073/pnas.1620089114

Pubmed 5603991

PMC 28808007

Senga, R.A., Alegria Terrazas, S., Balbirnie, K., Blank, M., Janiak, A., Szarejko, I., Chmielewska, B., Karcz, J., Morris, J., Hedley, P.E., George, T.S., and Bulgarelli, D. (2017) Root Hair Mutations Displace the Barley Rhizosphere Microbiota. Frontiers in plant science. 8, 1094

d.o.i 10.3389/fpls.2017.01094

Pubmed 5483447

PMC 28694814

Turnbull, D., and Hemsley, P.A. (2017) Fats and function: protein lipid modifications in plant cell signalling. Current opinion in plant biology. 40, 63-70

d.o.i 10.1016/j.pbi.2017.07.007

PMC 28772175

 Turnbull, D., Yang, L., Naqvi, S., Breen, S., Welsh, L., Stephens, J., Morris, J., Boevink, P.C., Hedley, P.E., Zhan, J., Birch, P.R.J., and Gilroy, E.M. (2017) RXLR Effector AVR2 Up-Regulates a Brassinosteroid-Responsive bHLH Transcription Factor to Suppress Immunity. Plant physiology. 174, 356-369

d.o.i 10.1104/pp.16.01804

Pubmed 5411136

PMC 28270626

Venuleo, M., Raven, J.A., and Giordano, M. (2017) Intraspecific chemical communication in microalgae. The New phytologist.

d.o.i 10.1111/nph.14524

PMC 28328079

 Wang, S., Boevink, P.C., Welsh, L., Zhang, R., Whisson, S.C., and Birch, P.R.J. (2017) Delivery of cytoplasmic and apoplastic effectors from Phytophthora infestans haustoria by distinct secretion pathways. The New phytologist. 216, 205-215

d.o.i 10.1111/nph.14696

Pubmed 5601276

PMC 28758684

 Wells, M.L., Potin, P., Craigie, J.S., Raven, J.A., Merchant, S.S., Helliwell, K.E., Smith, A.G., Camire, M.E., and Brawley, S.H. (2017) Algae as nutritional and functional food sources: revisiting our understanding. Journal of applied phycology. 29, 949-982

d.o.i 10.1007/s10811-016-0974-5

Pubmed 5387034

PMC 28458464

Williams, D., Britten, A., McCallum, S., Jones, H., Aitkenhead, M., Karley, A., Loades, K., Prashar, A., and Graham, J. (2017) A method for automatic segmentation and splitting of hyperspectral images of raspberry plants collected in field conditions. Plant methods. 13, 74

d.o.i 10.1186/s13007-017-0226-y

Pubmed 5664591

PMC 29118819

Zhang, R., Calixto, C.P.G., Marquez, Y., Venhuizen, P., Tzioutziou, N.A., Guo, W., Spensley, M., Entizne, J.C., Lewandowska, D., Ten Have, S., Frei Dit Frey, N., Hirt, H., James, A.B., Nimmo, H.G., Barta, A., Kalyna, M., and Brown, J.W.S. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic acids research. 45, 5061-5073

d.o.i 10.1093/nar/gkx267

Pubmed 5435985

PMC 28402429