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Items: 25

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.

Flow Sorting Plant Chromosomes.

Vrána J, Cápal P, Číhalíková J, Kubaláková M, Doležel J.

Methods Mol Biol. 2016;1429:119-34. doi: 10.1007/978-1-4939-3622-9_10.

PMID:
27511171
3.

Flow sorting and sequencing meadow fescue chromosome 4F.

Kopecký D, Martis M, Číhalíková J, Hřibová E, Vrána J, Bartoš J, Kopecká J, Cattonaro F, Stočes Š, Novák P, Neumann P, Macas J, Šimková H, Studer B, Asp T, Baird JH, Navrátil P, Karafiátová M, Kubaláková M, Šafář J, Mayer K, Doležel J.

Plant Physiol. 2013 Nov;163(3):1323-37. doi: 10.1104/pp.113.224105. Epub 2013 Oct 4.

4.

Flow cytometric chromosome sorting in plants: the next generation.

Vrána J, Simková H, Kubaláková M, Cíhalíková J, Doležel J.

Methods. 2012 Jul;57(3):331-7. doi: 10.1016/j.ymeth.2012.03.006. Epub 2012 Mar 14.

PMID:
22440520
5.

BAC libraries from wheat chromosome 7D: efficient tool for positional cloning of aphid resistance genes.

Simková H, Safář J, Kubaláková M, Suchánková P, Cíhalíková J, Robert-Quatre H, Azhaguvel P, Weng Y, Peng J, Lapitan NL, Ma Y, You FM, Luo MC, Bartoš J, Doležel J.

J Biomed Biotechnol. 2011;2011:302543. doi: 10.1155/2011/302543. Epub 2010 Dec 23.

6.

Chromosome analysis and sorting using flow cytometry.

Doležel J, Kubaláková M, Cíhalíková J, Suchánková P, Simková H.

Methods Mol Biol. 2011;701:221-38. doi: 10.1007/978-1-61737-957-4_12.

PMID:
21181533
7.

Development of chromosome-specific BAC resources for genomics of bread wheat.

Safár J, Simková H, Kubaláková M, Cíhalíková J, Suchánková P, Bartos J, Dolezel J.

Cytogenet Genome Res. 2010 Jul;129(1-3):211-23. doi: 10.1159/000313072. Epub 2010 May 26.

PMID:
20501977
8.

A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS).

Simková H, Safár J, Suchánková P, Kovárová P, Bartos J, Kubaláková M, Janda J, Cíhalíková J, Mago R, Lelley T, Dolezel J.

BMC Genomics. 2008 May 21;9:237. doi: 10.1186/1471-2164-9-237.

9.

Advanced resources for plant genomics: a BAC library specific for the short arm of wheat chromosome 1B.

Janda J, Safár J, Kubaláková M, Bartos J, Kovárová P, Suchánková P, Pateyron S, Cíhalíková J, Sourdille P, Simková H, Faivre-Rampant P, Hribová E, Bernard M, Lukaszewski A, Dolezel J, Chalhoub B.

Plant J. 2006 Sep;47(6):977-86. Epub 2006 Aug 15.

10.

Dissection of the nuclear genome of barley by chromosome flow sorting.

Suchánková P, Kubaláková M, Kovárová P, Bartos J, Cíhalíková J, Molnár-Láng M, Endo TR, Dolezel J.

Theor Appl Genet. 2006 Aug;113(4):651-9. Epub 2006 Jun 30.

PMID:
16810504
11.

Chromosome sorting in tetraploid wheat and its potential for genome analysis.

Kubaláková M, Kovárová P, Suchánková P, Cíhalíková J, Bartos J, Lucretti S, Watanabe N, Kianian SF, Dolezel J.

Genetics. 2005 Jun;170(2):823-9. Epub 2005 Mar 31.

12.

Construction of a subgenomic BAC library specific for chromosomes 1D, 4D and 6D of hexaploid wheat.

Janda J, Bartos J, Safár J, Kubaláková M, Valárik M, Cíhalíková J, Simková H, Caboche M, Sourdille P, Bernard M, Chalhoub B, Dolezel J.

Theor Appl Genet. 2004 Nov;109(7):1337-45. Epub 2004 Sep 10.

PMID:
15365624
13.

Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat.

Safár J, Bartos J, Janda J, Bellec A, Kubaláková M, Valárik M, Pateyron S, Weiserová J, Tusková R, Cíhalíková J, Vrána J, Simková H, Faivre-Rampant P, Sourdille P, Caboche M, Bernard M, Dolezel J, Chalhoub B.

Plant J. 2004 Sep;39(6):960-8.

14.

Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry.

Kubaláková M, Valárik M, Barto J, Vrána J, Cíhalíková J, Molnár-Láng M, Dolezel J.

Genome. 2003 Oct;46(5):893-905.

PMID:
14608406
15.

Flow karyotyping and chromosome sorting in bread wheat ( Triticum aestivum L.).

Kubaláková M, Vrána J, Cíhalíková J, Simková H, Dolezel J.

Theor Appl Genet. 2002 Jun;104(8):1362-1372. Epub 2002 Apr 10.

PMID:
12582592
16.

Development of flow cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.).

Vlácilová K, Ohri D, Vrána J, Cíhalíková J, Kubaláková M, Kahl G, Dolezel J.

Chromosome Res. 2002;10(8):695-706.

PMID:
12575797
17.

Localisation of DNA sequences on plant chromosomes using PRINS and C-PRINS.

Kubaláková M, Vrána J, Cíhalíková J, Lysák MA, Dolezel J.

Methods Cell Sci. 2001;23(1-3):71-82.

PMID:
11741145
18.

Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.).

Vrána J, Kubaláková M, Simková H, Cíhalíková J, Lysák MA, Dolezel J.

Genetics. 2000 Dec;156(4):2033-41.

19.

Rapid identification and determination of purity of flow-sorted plant chromosomes using C-PRINS.

Kubaláková M, Lysák MA, Vrána J, Simková H, Cíhalíková J, Dolezel J.

Cytometry. 2000 Oct 1;41(2):102-8.

PMID:
11002265
20.

Cell cycle synchronization in plant root meristems.

Dolezel J, Cíhalíková J, Weiserová J, Lucretti S.

Methods Cell Sci. 1999;21(2-3):95-107.

PMID:
10728642
21.

Flow karyotyping and sorting of mitotic chromosomes of barley (Hordeum vulgare L.).

Lysák MA, Cíhalíková J, Kubaláková M, Simková H, Künzel G, Dolezel J.

Chromosome Res. 1999;7(6):431-44.

PMID:
10560966
22.
23.

A high-yield procedure for isolation of metaphase chromosomes from root tips of Vicia faba L.

Doležel J, Cíhalíková J, Lucretti S.

Planta. 1992 Aug;188(1):93-8. doi: 10.1007/BF00198944.

PMID:
24178204
24.

Sequential estimation of nuclear DNA and silver staining of nucleoli in plant cells.

Dolezel J, Cíhalíková J, Zakchlenjuk OV.

Stain Technol. 1989 Jan;64(1):9-13.

PMID:
2472683
25.

Cytofluorometric determination of nuclear DNA in plant cells using auramine O.

Cíhalíková J, Dolezel J, Novák FJ.

Acta Histochem. 1985;76(2):151-6.

PMID:
3929543

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