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Items: 21

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.

Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides.

Akpinar BA, Biyiklioglu S, Alptekin B, Havránková M, Vrána J, Doležel J, Distelfeld A, Hernandez P; IWGSC, Budak H.

Plant Biotechnol J. 2018 Dec;16(12):2077-2087. doi: 10.1111/pbi.12940. Epub 2018 Jun 13.

3.

A large-scale multiomics analysis of wheat stem solidness and the wheat stem sawfly feeding response, and syntenic associations in barley, Brachypodium, and rice.

Biyiklioglu S, Alptekin B, Akpinar BA, Varella AC, Hofland ML, Weaver DK, Bothner B, Budak H.

Funct Integr Genomics. 2018 May;18(3):241-259. doi: 10.1007/s10142-017-0585-5. Epub 2018 Feb 22. Erratum in: Funct Integr Genomics. 2018 Sep;18(5):611.

4.

A Comprehensive Prescription for Plant miRNA Identification.

Alptekin B, Akpinar BA, Budak H.

Front Plant Sci. 2017 Jan 24;7:2058. doi: 10.3389/fpls.2016.02058. eCollection 2016.

5.

A large-scale chromosome-specific SNP discovery guideline.

Akpinar BA, Lucas S, Budak H.

Funct Integr Genomics. 2017 Jan;17(1):97-105. doi: 10.1007/s10142-016-0536-6. Epub 2016 Nov 29.

PMID:
27900504
6.

Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii.

Akpinar BA, Budak H.

Front Plant Sci. 2016 May 4;7:606. doi: 10.3389/fpls.2016.00606. eCollection 2016.

7.

Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia.

Kippes N, Debernardi JM, Vasquez-Gross HA, Akpinar BA, Budak H, Kato K, Chao S, Akhunov E, Dubcovsky J.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):E5401-10. doi: 10.1073/pnas.1514883112. Epub 2015 Aug 31.

8.

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress.

Akpinar BA, Kantar M, Budak H.

Funct Integr Genomics. 2015 Sep;15(5):587-98. doi: 10.1007/s10142-015-0453-0. Epub 2015 Jul 15.

PMID:
26174050
9.

Plant miRNAs: biogenesis, organization and origins.

Budak H, Akpinar BA.

Funct Integr Genomics. 2015 Sep;15(5):523-31. doi: 10.1007/s10142-015-0451-2. Epub 2015 Jun 26. Review.

PMID:
26113396
10.

Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides.

Akpinar BA, Yuce M, Lucas S, Vrána J, Burešová V, Doležel J, Budak H.

Sci Rep. 2015 Jun 18;5:10763. doi: 10.1038/srep10763.

11.

The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements.

Akpinar BA, Magni F, Yuce M, Lucas SJ, Šimková H, Šafář J, Vautrin S, Bergès H, Cattonaro F, Doležel J, Budak H.

BMC Genomics. 2015 Jun 13;16:453. doi: 10.1186/s12864-015-1641-y.

12.

Stress responsive miRNAs and isomiRs in cereals.

Budak H, Kantar M, Bulut R, Akpinar BA.

Plant Sci. 2015 Jun;235:1-13. doi: 10.1016/j.plantsci.2015.02.008. Epub 2015 Feb 20. Review.

PMID:
25900561
13.

Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum).

Akpinar BA, Lucas SJ, Vrána J, Doležel J, Budak H.

Plant Biotechnol J. 2015 Aug;13(6):740-52. doi: 10.1111/pbi.12302. Epub 2014 Dec 16.

14.

Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications.

Lucas SJ, Akpınar BA, Šimková H, Kubaláková M, Doležel J, Budak H.

BMC Genomics. 2014 Dec 9;15:1080. doi: 10.1186/1471-2164-15-1080.

15.

Genomics approaches for crop improvement against abiotic stress.

Akpınar BA, Lucas SJ, Budak H.

ScientificWorldJournal. 2013 Jun 6;2013:361921. doi: 10.1155/2013/361921. Print 2013. Review.

16.

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A.

Lucas SJ, Akpınar BA, Kantar M, Weinstein Z, Aydınoğlu F, Safář J, Simková H, Frenkel Z, Korol A, Magni F, Cattonaro F, Vautrin S, Bellec A, Bergès H, Doležel J, Budak H.

PLoS One. 2013 Apr 16;8(4):e59542. doi: 10.1371/journal.pone.0059542. Print 2013.

17.

Proteome changes in wild and modern wheat leaves upon drought stress by two-dimensional electrophoresis and nanoLC-ESI-MS/MS.

Budak H, Akpinar BA, Unver T, Turktas M.

Plant Mol Biol. 2013 Sep;83(1-2):89-103. doi: 10.1007/s11103-013-0024-5. Epub 2013 Feb 27.

PMID:
23443681
18.

Plant abiotic stress signaling.

Akpinar BA, Avsar B, Lucas SJ, Budak H.

Plant Signal Behav. 2012 Nov;7(11):1450-5. doi: 10.4161/psb.21894. Epub 2012 Sep 18. Review.

19.

Subgenomic analysis of microRNAs in polyploid wheat.

Kantar M, Akpınar BA, Valárik M, Lucas SJ, Doležel J, Hernández P, Budak H; International Wheat Genome Sequencing Consortium.

Funct Integr Genomics. 2012 Aug;12(3):465-79. doi: 10.1007/s10142-012-0285-0. Epub 2012 May 17.

PMID:
22592659
20.

Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response.

Kuzuoglu-Ozturk D, Cebeci Yalcinkaya O, Akpinar BA, Mitou G, Korkmaz G, Gozuacik D, Budak H.

Planta. 2012 Oct;236(4):1081-92. Epub 2012 May 9.

PMID:
22569921
21.

The drought response displayed by a DRE-binding protein from Triticum dicoccoides.

Lucas S, Durmaz E, Akpınar BA, Budak H.

Plant Physiol Biochem. 2011 Mar;49(3):346-51. doi: 10.1016/j.plaphy.2011.01.016. Epub 2011 Jan 21.

PMID:
21296583

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