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Items: 45

1.

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

International Wheat Genome Sequencing Consortium (IWGSC); IWGSC RefSeq principal investigators:, Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N; IWGSC whole-genome assembly principal investigators:, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG; Whole-genome sequencing and assembly:, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnère G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin AA; Hi-C data-based scaffolding:, Stein N, Mascher M, Himmelbach A; Whole-genome assembly quality control and analyses:, Choulet F, Keeble-Gagnère G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin AA, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V; Pseudomolecule assembly:, Choulet F, Keeble-Gagnère G, Mascher M, Josselin AA, Rogers J; RefSeq genome structure and gene analyses:, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnère G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Šimková H, Wicker T; Automated annotation:, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L; Manual gene curation:, Appels R, Rimbert H, Choulet F, Juhász A, Keeble-Gagnère G; Subgenome comparative analyses:, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnère G, Mayer KFX, Wicker T; Transposable elements:, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M; Phylogenomic analyses:, Lang D, Spannagl M, Appels R, Fischer I; Transcriptome analyses and RNA-seq data:, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH; Whole-genome methylome:, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A; Histone mark analyses:, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D; BAC chromosome MTP IWGSC–Bayer Whole-Genome Profiling (WGP) tags:, Rogers J, Jacobs J, Alaux M, Appels R, Bartoš J, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen OA, Šimková H, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S; Chromosome LTC mapping and physical mapping quality control:, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J; RH mapping:, Tiwari V, Gill B, Paux E, Poland J; Optical mapping:, Doležel J, Číhalíková J, Šimková H, Toegelová H, Vrána J; Recombination analyses:, Sourdille P, Darrier B; Gene family analyses:, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V; CBF gene family:, Barabaschi D, Cattivelli L; Dehydrin gene family:, Hernandez P, Galvez S, Budak H; NLR gene family:, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G; PPR gene family:, Small I, Melonek J, Zhou R; Prolamin gene family:, Juhász A, Belova T, Appels R, Olsen OA; WAK gene family:, Kanyuka K, King R; Stem solidness (SSt1) QTL team:, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D; Flowering locus C (FLC) gene team:, Rohde A, Golds T; Genome size analysis:, Doležel J, Čížková J, Tibbits J; MicroRNA and tRNA annotation:, Budak H, Akpinar BA, Biyiklioglu S; Genetic maps and mapping:, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A; BAC libraries and chromosome sorting:, Doležel J, Šimková H, Číhalíková J, Kubaláková M, Šafář J, Vrána J; BAC pooling, BAC library repository, and access:, Berges H, Bellec A, Vautrin S; IWGSC sequence and data repository and access:, Alaux M, Alfama F, Adam-Blondon AF, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H; Physical maps and BAC-based sequences:; 1A BAC sequencing and assembly:, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T; 1B BAC sequencing and assembly:, Choulet F, Paux E, Alberti A, Aury JM, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P; 1D, 4D, and 6D physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 2AL physical mapping:, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B; 2AS physical mapping:, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS; 2B, 2D, 4B, 5BL, and 5DL IWGSC–Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S; 3AL physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 3DS physical mapping and BAC sequencing and assembly:, Bartoš J, Holušová K, Plíhal O; 3DL BAC sequencing and assembly:, Clark MD, Heavens D, Kettleborough G, Wright J; 4A physical mapping, BAC sequencing, assembly, and annotation:, Valárik M, Abrouk M, Balcárková B, Holušová K, Hu Y, Luo M; 5BS BAC sequencing and assembly:, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E; 6B BAC sequencing and assembly:, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J; 7A physical mapping and BAC sequencing:, Appels R, Hayden M, Keeble-Gagnère G, Rigault P, Tibbits J; 7B physical mapping, BAC sequencing, and assembly:, Olsen OA, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B; 7DS BAC sequencing and assembly:, Šimková H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelová H, Tulpová Z, Visendi P; 7DL physical mapping and BAC sequencing:, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L; Figures:, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L; Manuscript writing team:, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Šimková H, Small I, Spannagl M, Swarbreck D, Uauy C.

Science. 2018 Aug 17;361(6403). pii: eaar7191. doi: 10.1126/science.aar7191. Epub 2018 Aug 16.

PMID:
30115783
2.

Foxtail mosaic virus: A Viral Vector for Protein Expression in Cereals.

Bouton C, King RC, Chen H, Azhakanandam K, Bieri S, Hammond-Kosack KE, Kanyuka K.

Plant Physiol. 2018 Aug;177(4):1352-1367. doi: 10.1104/pp.17.01679. Epub 2018 Jun 7.

PMID:
29880705
3.

Wheat receptor-kinase-like protein Stb6 controls gene-for-gene resistance to fungal pathogen Zymoseptoria tritici.

Saintenac C, Lee WS, Cambon F, Rudd JJ, King RC, Marande W, Powers SJ, Bergès H, Phillips AL, Uauy C, Hammond-Kosack KE, Langin T, Kanyuka K.

Nat Genet. 2018 Mar;50(3):368-374. doi: 10.1038/s41588-018-0051-x. Epub 2018 Feb 12.

PMID:
29434355
4.

Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat.

Chen J, Upadhyaya NM, Ortiz D, Sperschneider J, Li F, Bouton C, Breen S, Dong C, Xu B, Zhang X, Mago R, Newell K, Xia X, Bernoux M, Taylor JM, Steffenson B, Jin Y, Zhang P, Kanyuka K, Figueroa M, Ellis JG, Park RF, Dodds PN.

Science. 2017 Dec 22;358(6370):1607-1610. doi: 10.1126/science.aao4810.

PMID:
29269475
5.

RNAi as an emerging approach to control Fusarium head blight disease and mycotoxin contamination in cereals.

Machado AK, Brown NA, Urban M, Kanyuka K, Hammond-Kosack KE.

Pest Manag Sci. 2018 Apr;74(4):790-799. doi: 10.1002/ps.4748. Epub 2017 Nov 22. Review.

6.

Characterization of an antimicrobial and phytotoxic ribonuclease secreted by the fungal wheat pathogen Zymoseptoria tritici.

Kettles GJ, Bayon C, Sparks CA, Canning G, Kanyuka K, Rudd JJ.

New Phytol. 2018 Jan;217(1):320-331. doi: 10.1111/nph.14786. Epub 2017 Sep 12.

7.

A new proteinaceous pathogen-associated molecular pattern (PAMP) identified in Ascomycete fungi induces cell death in Solanaceae.

Franco-Orozco B, Berepiki A, Ruiz O, Gamble L, Griffe LL, Wang S, Birch PRJ, Kanyuka K, Avrova A.

New Phytol. 2017 Jun;214(4):1657-1672. doi: 10.1111/nph.14542. Epub 2017 Apr 7.

8.

Sequence diversification in recessive alleles of two host factor genes suggests adaptive selection for bymovirus resistance in cultivated barley from East Asia.

Yang P, Habekuß A, Hofinger BJ, Kanyuka K, Kilian B, Graner A, Ordon F, Stein N.

Theor Appl Genet. 2017 Feb;130(2):331-344. doi: 10.1007/s00122-016-2814-z. Epub 2016 Nov 9.

9.

Apoplastic recognition of multiple candidate effectors from the wheat pathogen Zymoseptoria tritici in the nonhost plant Nicotiana benthamiana.

Kettles GJ, Bayon C, Canning G, Rudd JJ, Kanyuka K.

New Phytol. 2017 Jan;213(1):338-350. doi: 10.1111/nph.14215. Epub 2016 Oct 3.

10.

The genome of the emerging barley pathogen Ramularia collo-cygni.

McGrann GR, Andongabo A, Sjökvist E, Trivedi U, Dussart F, Kaczmarek M, Mackenzie A, Fountaine JM, Taylor JM, Paterson LJ, Gorniak K, Burnett F, Kanyuka K, Hammond-Kosack KE, Rudd JJ, Blaxter M, Havis ND.

BMC Genomics. 2016 Aug 9;17:584. doi: 10.1186/s12864-016-2928-3.

11.

A Metabolic Gene Cluster in the Wheat W1 and the Barley Cer-cqu Loci Determines β-Diketone Biosynthesis and Glaucousness.

Hen-Avivi S, Savin O, Racovita RC, Lee WS, Adamski NM, Malitsky S, Almekias-Siegl E, Levy M, Vautrin S, Bergès H, Friedlander G, Kartvelishvily E, Ben-Zvi G, Alkan N, Uauy C, Kanyuka K, Jetter R, Distelfeld A, Aharoni A.

Plant Cell. 2016 Jun;28(6):1440-60. doi: 10.1105/tpc.16.00197. Epub 2016 May 25.

12.

Dissecting the Molecular Interactions between Wheat and the Fungal Pathogen Zymoseptoria tritici.

Kettles GJ, Kanyuka K.

Front Plant Sci. 2016 Apr 15;7:508. doi: 10.3389/fpls.2016.00508. eCollection 2016. Review.

13.

G-protein α-subunit (GPA1) regulates stress, nitrate and phosphate response, flavonoid biosynthesis, fruit/seed development and substantially shares GCR1 regulation in A. thaliana.

Chakraborty N, Sharma P, Kanyuka K, Pathak RR, Choudhury D, Hooley R, Raghuram N.

Plant Mol Biol. 2015 Dec;89(6):559-76. doi: 10.1007/s11103-015-0374-2. Epub 2015 Sep 7.

PMID:
26346778
14.
15.

Plant virus particles carrying tumour antigen activate TLR7 and Induce high levels of protective antibody.

Jobsri J, Allen A, Rajagopal D, Shipton M, Kanyuka K, Lomonossoff GP, Ottensmeier C, Diebold SS, Stevenson FK, Savelyeva N.

PLoS One. 2015 Feb 18;10(2):e0118096. doi: 10.1371/journal.pone.0118096. eCollection 2015.

16.

Transcriptome analysis of Arabidopsis GCR1 mutant reveals its roles in stress, hormones, secondary metabolism and phosphate starvation.

Chakraborty N, Sharma P, Kanyuka K, Pathak RR, Choudhury D, Hooley RA, Raghuram N.

PLoS One. 2015 Feb 10;10(2):e0117819. doi: 10.1371/journal.pone.0117819. eCollection 2015. Erratum in: PLoS One. 2015;10(3):e0122423.

17.

Functional analysis of a Wheat Homeodomain protein, TaR1, reveals that host chromatin remodelling influences the dynamics of the switch to necrotrophic growth in the phytopathogenic fungus Zymoseptoria tritici.

Lee J, Orosa B, Millyard L, Edwards M, Kanyuka K, Gatehouse A, Rudd J, Hammond-Kosack K, Pain N, Sadanandom A.

New Phytol. 2015 Apr;206(2):598-605. doi: 10.1111/nph.13323. Epub 2015 Jan 30.

18.

Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition.

Rudd JJ, Kanyuka K, Hassani-Pak K, Derbyshire M, Andongabo A, Devonshire J, Lysenko A, Saqi M, Desai NM, Powers SJ, Hooper J, Ambroso L, Bharti A, Farmer A, Hammond-Kosack KE, Dietrich RA, Courbot M.

Plant Physiol. 2015 Mar;167(3):1158-85. doi: 10.1104/pp.114.255927. Epub 2015 Jan 16.

19.

Deregulation of Plant Cell Death Through Disruption of Chloroplast Functionality Affects Asexual Sporulation of Zymoseptoria tritici on Wheat.

Lee WS, Devonshire BJ, Hammond-Kosack KE, Rudd JJ, Kanyuka K.

Mol Plant Microbe Interact. 2015 May;28(5):590-604. doi: 10.1094/MPMI-10-14-0346-R. Epub 2015 Apr 22.

20.

Genetic analyses of BaMMV/BaYMV resistance in barley accession HOR4224 result in the identification of an allele of the translation initiation factor 4e (Hv-eIF4E) exclusively effective against Barley mild mosaic virus (BaMMV).

Perovic D, Krämer I, Habekuss A, Perner K, Pickering R, Proeseler G, Kanyuka K, Ordon F.

Theor Appl Genet. 2014 May;127(5):1061-71. doi: 10.1007/s00122-014-2279-x. Epub 2014 Feb 13.

PMID:
24522725
21.

Mycosphaerella graminicola LysM effector-mediated stealth pathogenesis subverts recognition through both CERK1 and CEBiP homologues in wheat.

Lee WS, Rudd JJ, Hammond-Kosack KE, Kanyuka K.

Mol Plant Microbe Interact. 2014 Mar;27(3):236-43. doi: 10.1094/MPMI-07-13-0201-R.

22.
23.

An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.

Hofinger BJ, Russell JR, Bass CG, Baldwin T, dos Reis M, Hedley PE, Li Y, Macaulay M, Waugh R, Hammond-Kosack KE, Kanyuka K.

Mol Ecol. 2011 Sep;20(17):3653-68. doi: 10.1111/j.1365-294X.2011.05201.x. Epub 2011 Aug 2.

PMID:
21806691
24.

Inactivation of plant infecting fungal and viral pathogens to achieve biological containment in drainage water using UV treatment.

Urban M, Motteram J, Jing HC, Powers S, Townsend J, Devonshire J, Pearman I, Kanyuka K, Franklin J, Hammond-Kosack KE.

J Appl Microbiol. 2011 Mar;110(3):675-87. doi: 10.1111/j.1365-2672.2010.04917.x. Epub 2011 Jan 13.

25.

DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum.

Jing HC, Bayon C, Kanyuka K, Berry S, Wenzl P, Huttner E, Kilian A, Hammond-Kosack KE.

BMC Genomics. 2009 Sep 30;10:458. doi: 10.1186/1471-2164-10-458.

26.

High-resolution melting analysis of cDNA-derived PCR amplicons for rapid and cost-effective identification of novel alleles in barley.

Hofinger BJ, Jing HC, Hammond-Kosack KE, Kanyuka K.

Theor Appl Genet. 2009 Sep;119(5):851-65. doi: 10.1007/s00122-009-1094-2. Epub 2009 Jul 4.

PMID:
19578831
27.

Characterization of two unusual features of resistance to soilborne cereal mosaic virus in hexaploid wheat: leakiness and gradual elimination of viral coat protein from infected root tissues.

Lyons R, Yilmaz ND, Powers S, Hammond-Kosack KE, Kanyuka K.

Mol Plant Microbe Interact. 2009 May;22(5):560-74. doi: 10.1094/MPMI-22-5-0560.

28.

Identification and characterization of a novel efficient resistance response to the furoviruses SBWMV and SBCMV in barley.

Lyons R, Hammond-Kosack KE, Kanyuka K.

Mol Plant Microbe Interact. 2008 Sep;21(9):1193-204. doi: 10.1094/MPMI-21-9-1193.

29.

GCN2-dependent phosphorylation of eukaryotic translation initiation factor-2alpha in Arabidopsis.

Zhang Y, Wang Y, Kanyuka K, Parry MA, Powers SJ, Halford NG.

J Exp Bot. 2008;59(11):3131-41. doi: 10.1093/jxb/ern169. Epub 2008 Jul 4.

30.

Identification of variation in adaptively important traits and genome-wide analysis of trait-marker associations in Triticum monococcum.

Jing HC, Kornyukhin D, Kanyuka K, Orford S, Zlatska A, Mitrofanova OP, Koebner R, Hammond-Kosack K.

J Exp Bot. 2007;58(13):3749-64.

PMID:
18057045
31.

The Sbm1 locus conferring resistance to Soil-borne cereal mosaic virus maps to a gene-rich region on 5DL in wheat.

Bass C, Hendley R, Adams MJ, Hammond-Kosack KE, Kanyuka K.

Genome. 2006 Sep;49(9):1140-8.

PMID:
17110994
32.
33.

Evidence that the recessive bymovirus resistance locus rym4 in barley corresponds to the eukaryotic translation initiation factor 4E gene.

Kanyuka K, Druka A, Caldwell DG, Tymon A, McCallum N, Waugh R, Adams MJ.

Mol Plant Pathol. 2005 Jul 1;6(4):449-58. doi: 10.1111/j.1364-3703.2005.00294.x.

PMID:
20565670
34.
35.

Biological and sequence analysis of a novel European isolate of Barley mild mosaic virus that overcomes the barley rym5 resistance gene.

Kanyuka K, McGrann G, Alhudaib K, Hariri D, Adams MJ.

Arch Virol. 2004 Aug;149(8):1469-80. Epub 2004 Apr 5.

PMID:
15290374
36.
37.

Polymyxa graminis and the cereal viruses it transmits: a research challenge.

Kanyuka K, Ward E, Adams MJ.

Mol Plant Pathol. 2003 Sep 1;4(5):393-406. doi: 10.1046/j.1364-3703.2003.00177.x.

PMID:
20569399
38.

Mutations in the huge Arabidopsis gene BIG affect a range of hormone and light responses.

Kanyuka K, Praekelt U, Franklin KA, Billingham OE, Hooley R, Whitelam GC, Halliday KJ.

Plant J. 2003 Jul;35(1):57-70.

39.

Homologues of a single resistance-gene cluster in potato confer resistance to distinct pathogens: a virus and a nematode.

van der Vossen EA, van der Voort JN, Kanyuka K, Bendahmane A, Sandbrink H, Baulcombe DC, Bakker J, Stiekema WJ, Klein-Lankhorst RM.

Plant J. 2000 Sep;23(5):567-76.

40.
41.

The Rx gene from potato controls separate virus resistance and cell death responses.

Bendahmane A, Kanyuka K, Baulcombe DC.

Plant Cell. 1999 May;11(5):781-92.

42.

Nucleotide sequence of shallot virus X RNA reveals a 5'-proximal cistron closely related to those of potexviruses and a unique arrangement of the 3'-proximal cistrons.

Kanyuka KV, Vishnichenko VK, Levay KE, Kondrikov DYu, Ryabov EV, Zavriev SK.

J Gen Virol. 1992 Oct;73 ( Pt 10):2553-60.

PMID:
1339468
43.

The genome organization of potato virus M RNA.

Zavriev SK, Kanyuka KV, Levay KE.

J Gen Virol. 1991 Jan;72 ( Pt 1):9-14.

PMID:
1990070
44.

The putative RNA replicase of potato virus M: obvious sequence similarity with potex- and tymoviruses.

Morozov SYu, Kanyuka KV, Levay KE, Zavriev SK.

Virology. 1990 Dec;179(2):911-4.

PMID:
2238481
45.

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