Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.

Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany Sokolovská 6 Olomouc Czech Republic

Zobrazit více v PubMed

lkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods. 2011;8:61–65. PubMed PMC

Ananiev GE, Goldstein S, Runnheim R, Forrest DK, Zhou SG, Potamousis K, Churas CP, Bergendahl V, Thomson JA, Schwartz DC. Optical mapping discerns genome wide DNA methylation profiles. BMC Mol Biol. 2008;9:68–81. PubMed PMC

Arumuganathan K, Slattery JP, Tanksley SD, Earle ED. Preparation and flow cytometric analysis of metaphase chromosomes of tomato. Theor Appl Genet. 1991;82:101–111. PubMed

Arumuganathan K, Martin GB, Telenius H, Tanksley SD, Earle ED. Chromosome 2-specific DNA clones from flow-sorted chromosomes of tomato. Mol Gen Genet. 1994;242:551–558. PubMed

Aten JA, Buys CHCM, Vanderveen AY, Mesa JR, Yu LC, Gray JW, Osinga J, Stap J. Stabilization of chromosomes by DNA intercalators for flow karyotyping and identification by banding of isolated chromosomes. Histochemistry. 1987;87:359–366. PubMed

Aten JA, Kooi MW, Stap J, Kipp JBA, Barendsen GW. X-ray-induced and neutron-induced chromosome-damage detected by flow-cytometry compared to cell lethality and chromosome structural-changes. Radiat Res. 1987;110:329–339. PubMed

Barigozzi C. Experiments with microdissection of the chromosome of the salivary glands of Chironomus sp. Archiv Exp Zellforsch. 1939;22:190–194.

Baron B, Metezeau P, Kiefergachelin H, Goldberg ME. Construction and characterization of a DNA library from mouse chromosomes-19 purified by flow-cytometry. Biol Cell. 1990;69:1–8. PubMed

Bartholdi MF. Flow cytogenetics. Pathobiology. 1990;58:118–128. PubMed

Bartholdi MF, Meyne J, Johnston RG, Cram LS. Chromosome-banding analysis by slit-scan flow-cytometry. Cytometry. 1989;10:124–133. PubMed

Bartholdi MF, Parson JD, Albright KA, Cram LS. System for flow sorting chromosomes on the basis of pulse shape. Cytometry. 1990;11:165–172. PubMed

Bartoš J, Paux E, Kofler R, Havránková M, Kopecký D, Suchánková P, Šafář J, Šimková H, Town CD, Lelley T, Feuillet C, Doležel J. A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. BMC Plant Biol. 2008;8:95–106. PubMed PMC

Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EY, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J, Edwards D. Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J. 2011;9:768–775. PubMed

Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Hernandez P, Edwards D. Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet. 2012;124:423–432. PubMed

Bijman JT. Optimization of mammalian chromosome suspension preparations employed in a flow cytometric analysis. Cytometry. 1983;3:354–358. PubMed

Binarová P, Hause B, Doležel J, Dráber P. Association of γ-tubulin with kinetochore/centromeric region of plant chromosomes. Plant J. 1998;14:751–757.

Birchler J, Gao Z, Han FP. A tale of two centromeres—diversity of structure but conservation of function in plants and animals. Funct Integr Genom. 2009;9:7–13. PubMed

Birchler JA, Krishnaswamy L, Gaeta RT, Masonbrink RE, Zhao CZ. Engineered minichromosomes in plants. Crit Rev Plant Sci. 2010;2:135–147.

Blennow E. Reverse painting highlights the origin of chromosome aberrations. Chromosom Res. 2004;12:25–33. PubMed

Boschman GA, Manders EMM, Rens W, Slater R, Aten JA. Semiautomated detection of aberrant chromosomes in bivariate flow karyotypes. Cytometry. 1992;13:469–477. PubMed

Bouvet A, Konfortov BA, Miller NGA, Brown D, Tucker EM. Identification of pig chromosomes in pig–mouse somatic-cell hybrid bivariate flow karyotypes. Cytometry. 1993;14:369–376. PubMed

Brar GA, Amon A. Emerging roles for centromeres in meiosis I chromosome segregation. Nat Rev Genet. 2008;9:899–910. PubMed PMC

Brind’Amour J, Lansdorp PM. Analysis of repetitive DNA in chromosomes by flow cytometry. Nat Methods. 2011;8:484–486. PubMed PMC

Carrano AV, Gray JW, Moore DH, Minkler JL, Mayall BH, Van Dilla MA, Mendelsohn ML. Purification of the chromosomes of the Indian muntjac by flow sorting. J Histochem Cytochem. 1976;24:348–354. PubMed

Carrano AV, Gray JW, Langlois RG, Burkhartschultz KJ, Van Dilla MA. Measurement and purification of human-chromosomes by flow cytometry and sorting. Proc Natl Acad Sci USA. 1979;76:1382–1384. PubMed PMC

Carter NP. Gene mapping and PCR application with flow-sorted chromosomes. In: Jacquemin-Sablon A, editor. Flow cytometry. Berlin: Springer; 1993. pp. 327–341.

Carter NP, Ferguson-Smith MA, Perryman MT, Telenius H, Pelmear AH, Leversha MA, Glancy MT, Wood SL, Cook K, Dyson HM. Reverse chromosome painting: a method for the rapid analysis of aberrant chromosomes in clinical cytogenetics. J Med Genet. 1992;29:299–307. PubMed PMC

Chambers R, Sands C. A dissection of the chromosomes in the pollen mother cells of Tradescantia virginiana. J Gen Physiol. 1923;5:815–821. PubMed PMC

Chang KS, Vyas RC, Deaven LL, Trujillo JM, Stass SA, Hittelman WN. PCR amplification of chromosome-specific DNA isolated from flow cytometry-sorted chromosomes. Genomics. 1992;12:307–312. PubMed

Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, Schulz MH, Erdogan F, Li N, Kijas Z, Arkesteijn G, Pajares IL, Goetz-Sothmann M, Heinrich U, Rost I, Dufke A, Grasshoff U, Glaeser B, Vingron M, Ropers HH. Mapping translocation breakpoints by next-generation sequencing. Genome Res. 2008;18:1143–1149. PubMed PMC

Chen W, Ullmann R, Langnick C, Menzel C, Wotschofsky Z, Hu H, Döring A, Hu Y, Kang H, Tzschach A, Hoeltzenbein M, Neitzel H, Markus S, Wiedersberg E, Kistner G, van Ravenswaaij-Arts CM, Kleefstra T, Kalscheuer VM, Ropers HH. Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing. Eur J Hum Genet. 2010;18:539–543. PubMed PMC

Conia J, Bergounioux C, Perennes C, Muller P, Brown S, Gadal P. Flow cytometric analysis and sorting of plant chromosomes from Petunia hybrida protoplasts. Cytometry. 1987;8:500–508. PubMed

Conia J, Muller P, Brown S, Bergounioux C, Gadal P. Monoparametric models of flow cytometric karyotypes with spreadsheet software. Theor Appl Genet. 1989;77:295–303. PubMed

Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Wellcome Trust Case Control C, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME. Origins and functional impact of copy number variation in the human genome. Nature. 2010;464:704–712. PubMed PMC

Cotter F, Nasipuri S, Lam G, Young BD. Gene mapping by enzymatic amplification from flow-sorted chromosomes. Genomics. 1989;5:470–475. PubMed

Cram LS, Bartholdi MF, Ray FA, Travis GL, Kraemer PM. Spontaneous neoplastic evolution of Chinese-hamster cells in culture—multistep progression of karyotype. Cancer Res. 1983;43:4828–4837. PubMed

Cram LS, Bell CS, Fawcett JJ. Chromosome sorting and genomics. Methods Cell Sci. 2002;24:27–35. PubMed

Cremer T, Lichter P, Borden J, Ward DC, Manuelidis L. Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes. Hum Genet. 1988;80:235–246. PubMed

Crosland MWJ, Crozier RH. Myrmecia pilosula, an ant with only one pair of chromosomes. Science. 1986;231:1278. PubMed

Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin SF, Brenton JD, Tavare S, Caldas C. The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics. 2009;10:588–610. PubMed PMC

Das SK, Austin MD, Akana MC, Deshpande P, Cao H, Xiao M. Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes. Nucleic Acids Res. 2010;38:e177. PubMed PMC

Davies KE, Young BD, Elles RG, Hill ME, Williamson R. Cloning of a representative genomic library of the human X chromosome after sorting by flow cytometry. Nature. 1981;293:374–376. PubMed

de Jong JH, Fransz P, Zabel P. High resolution FISH in plants—techniques and applications. Trends Plant Sci. 1999;4:258–263. PubMed

de Laat AMM, Blaas J. Flow-cytometric characterization and sorting of plant chromosomes. Theor Appl Genet. 1984;67:463–467. PubMed

de Laat AMM, Schel JHN. The integrity of metaphase chromosomes of Haplopappus gracilis (Nutt) Gray isolated by flow cytometry. Plant Sci. 1986;47:145–151.

Di Bucchianico S, Poma AM, Giardi MF, Di Leandro L, Valle F, Biscarini F, Botti D. Atomic force microscope nanolithography on chromosomes to generate single-cell genetic probes. J Nanobiotechnol. 2011;9:27–33. PubMed PMC

Doležel J, Lucretti S. High-resolution flow karyotyping and chromosome sorting in Vicia faba lines with standard and reconstructed karyotypes. Theor Appl Genet. 1995;90:797–802. PubMed

Doležel J, Číhalíková J, Lucretti S. A high-yield procedure for isolation of metaphase chromosomes from root tips of Vicia faba L. Planta. 1992;188:93–98. PubMed

Doležel J, Lucretti S, Schubert I. Plant chromosome analysis and sorting by flow cytometry. Crit Rev Plant Sci. 1994;13:275–309.

Doležel J, Kubaláková M, Bartoš J, Macas J. Flow cytogenetics and plant genome mapping. Chromosom Res. 2004;12:77–91. PubMed

Dudin G, Cremer T, Schardin M, Hausmann M, Bier F, Cremer C. A method for nucleic acid hybridization to isolated chromosomes in suspension. Hum Genet. 1987;76:290–292. PubMed

Dudin G, Steegmayer EW, Vogt P, Schnitzer H, Diaz E, Howell KE, Cremer T, Cremer C. Sorting of chromosomes by magnetic separation. Hum Genet. 1988;80:111–116. PubMed

Duncan A, Hadlaczky G. Chromosomal engineering. Curr Opin Biotechnol. 2007;18:420–424. PubMed

Fan HC, Wang JB, Potanina A, Quake SR. Whole-genome molecular haplotyping of single cells. Nat Biotechnol. 2011;29:51–57. PubMed PMC

Fantes JA, Green DK, Elder JK, Malloy P, Evans HJ. Detecting radiation damage to human chromosomes by flow cytometry. Mutat Res. 1983;119:161–168. PubMed

Fantes JA, Green DK, Malloy P, Sumner AT. Flow-cytometry measurements of human-chromosome kinetochore labeling. Cytometry. 1989;10:134–142. PubMed

Ferguson-Smith MA. Genetic analysis by chromosome sorting and painting: phylogenetic and diagnostic applications. Eur J Hum Genet. 1997;5:253–265. PubMed

Ferguson-Smith MA, Trifonov V. Mammalian karyotype evolution. Nat Rev Genet. 2007;8:950–962. PubMed

Feuillet C, Eversole K. Physical mapping of the wheat genome: a coordinated effort to lay the foundation for genome sequencing and develop tools for breeders. Isr J Plant Sci. 2007;55:307–313.

Fiegler H, Gribble SM, Burford DC, Carr P, Prigmore E, Porter KM, Clegg S, Crolla JA, Dennis NR, Jacobs P, Carter NP. Array painting: a method for the rapid analysis of aberrant chromosomes using DNA microarrays. J Med Genet. 2003;40:664–670. PubMed PMC

Fluch S, Kopecky D, Burg K, Šimková H, Taudien S, Petzold A, Kubaláková M, Platzer M, Berenyi M, Krainer S, Doležel J, Lelley T. Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1. PLoS One. 2012;7:e30784. PubMed PMC

Fuchs J, Houben A, Brandes A, Schubert I. Chromosome ‘painting’ in plants—a feasible technique? Chromosoma. 1996;104:315–320. PubMed

Fukui K. Structural analyses of chromosomes and their constituent proteins. Cytogenet Genome Res. 2009;124:215–227. PubMed

Gill KS, Arumuganathan K, Le JH. Isolating individual wheat (Triticum aestivum) chromosome arm by flow cytometric analysis of ditelosomic lines. Theor Appl Genet. 1999;98:1248–1252.

Gingrich JC, Boehrer DM, Garnes JA, Johnson W, Wong BS, Bergmann A, Eveleth GG, Langlois RG, Carrano AV. Construction and characterization of human chromosome 2-specific cosmid, fosmid, and PAC clone libraries. Genomics. 1996;32:65–74. PubMed

Gordon DJ, Resio B, Pellman D. Causes and consequences of aneuploidy in cancer. Nat Rev Genet. 2012;13:189–203. PubMed

Goyal A, Bhowmik PK, Basu SK. Minichromosomes: the second generation genetic engineering tool. Plant Omics. 2009;2:1–8.

Grady DL, Robinson DL, Gersh M, Nickerson E, McPherson J, Wasmuth JJ, Overhauser J, Deaven LL, Moyzis RK. The generation and regional localization of 303 new chromosome 5 sequence-tagged sites. Genomics. 1996;32:91–96. PubMed

Gray JW. Flow cytogenetics. New York: Academic; 1989.

Gray JW, Cram LS. Flow karyotyping and chromosome sorting. In: Melamed MR, Mendelsohn ML, editors. Flow cytometry and chromosome sorting. New York: Wiley-Liss; 1990. pp. 503–529.

Gray JW, Carrano AV, Steinmetz LL, Van Dilla MA, Moore HH, Mayall BH, Mendelsohn ML. Chromosome measurement and sorting by flow systems. Proc Natl Acad Sci USA. 1975;72:1231–1234. PubMed PMC

Gray JW, Carrano AV, Moore HH, Steinmetz LL, Minkler J, Mayall BH, Mendelsohn ML, Van Dilla MA. High-speed quantitative karyotyping by flow microfluorometry. Clin Chem. 1975;21:1258–1262. PubMed

Gray JW, Lucas J, Peters D, Pinkel D, Trask B, van den Engh G, Van Dilla M. Flow karyotyping and sorting of human chromosomes. Cold Spring Harb Symp Quant Biol. 1986;51:141–149. PubMed

Gribble SM, Ng BL, Prigmore E, Burford DC, Carter NP. Chromosome paints from single copies of chromosomes. Chromosom Res. 2004;12:143–151. PubMed

Gualberti G, Doležel J, Macas J, Lucretti S. Preparation of pea (Pisum sativum L.) chromosome and nucleus suspensions from single root tips. Theor Appl Genet. 1996;92:744–751. PubMed

Gygi MP, Ferguson MD, Mefford HC, Lund KP, O’Day C, Zhou P, Friedman C, van den Engh G, Stolowitz ML, Trask BJ. Use of fluorescent sequence-specific polyamides to discriminate human chromosomes by microscopy and flow cytometry. Nucleic Acids Res. 2002;30:2790–2799. PubMed PMC

Han YH, Zhang ZH, Huang SW, Jin WW. An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2. BMC Genet. 2011;12:18–24. PubMed PMC

Harris P, Boyd E, Ferguson-Smith MA. Optimising human chromosome separation for the production of chromosome-specific DNA libraries by flow sorting. Hum Genet. 1985;70:59–65. PubMed

Harris P, Morton CC, Guglielmi P, Li F, Kelly K, Latt SA. Mapping by chromosome sorting of several gene probes, including c-myc, to the derivative chromosomes of a 3;8 translocation associated with familial renal cancer. Cytometry. 1986;7:589–594. PubMed

Hausmann M, Popescu CP, Boscher J, Kerboeuf D, Dölle J, Cremer C. Identification and cytogenetic analysis of an abnormal pig chromosome for flow cytometry and sorting. Z Naturforsch C. 1993;48:645–653. PubMed

Hernandez P, Martis M, Dorado G, Pfeifer M, Gálvez S, Schaaf S, Jouve N, Šimková H, Valárik M, Doležel J, Mayer KFX. Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J. 2012;69:377–386. PubMed

Heslop-Harrison JS, Schwarzacher T. Organisation of the plant genome in chromosomes. Plant J. 2011;66:18–33. PubMed

Hobza R, Vyskot B. Laser microdissection-based analysis of plant sex chromosomes. Methods Cell Biol. 2007;82:433–453. PubMed

Hoshiya H, Kazuki Y, Abe S, Takiguchi M, Kajitani N, Watanabe Y, Yoshino T, Shirayoshi Y, Higaki K, Messina G, Cossu G, Oshimura M. A highly stable and nonintegrated human artificial chromosome (HAC) containing the 2.4 Mb entire human dystrophin gene. Mol Ther. 2009;17:309–317. PubMed PMC

Hui SM, Trask B, Vandenengh G, Bartuski AJ, Smith A, Flint A, Lalande M, Silverman GA. Analysis of randomly amplified flow-sorted chromosomes using the polymerase chain-reaction. Genomics. 1995;26:364–371. PubMed

International Wheat Genome Sequencing Consortium. http://www.wheatgenome.org/. Accessed on 14 March 2012.

Jaccoud D, Peng K, Feinstein D, Kilian A. Diversity Arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res. 2001;29:25–31. PubMed PMC

Janda J, Šafář J, Kubaláková M, Bartoš J, Kovářová P, Suchánková P, Pateyron S, Číhalíková J, Sourdille P, Šimková H, Fairaivre-Rampant P, Hřibová E, Bernard M, Lukaszewski A, Doležel J, Chalhoub B. Advanced resources for plant genomics: BAC library specific for the short arm of wheat chromosome 1B. Plant J. 2006;47:977–986. PubMed

Kamnasaran D, O’Brien PCM, Schuffenhauer S, Quarrell O, Lupski JR, Grammatico P, Ferguson-Smith MA, Cox DW. Defining the breakpoints of proximal chromosome 14q rearrangements in nine patients using flow-sorted chromosomes. Am J Med Genet. 2001;102:173–182. PubMed

Kejnovský E, Vrána J, Matsunaga S, Souček P, Široký J, Doleže J, Vyskot B. Localization of male-specifically expressed MROS genes of Silene latifolia by PCR on flow-sorted sex chromosomes and autosomes. Genetics. 2001;158:1269–1277. PubMed PMC

Kemkemer C, Kohn M, Kehrer-Sawatzki H, Minich P, Hogel J, Froenicke L, Hameister H. Reconstruction of the ancestral ferungulate karyotype by electronic chromosome painting (E-painting) Chromosom Res. 2006;14:899–907. PubMed

Kim UJ, Shizuya H, Birren B, Slepak T, deJong P, Simon MI. Selection of chromosome 22-specific clones from human genomic BAC library using a chromosome-specific cosmid library pool. Genomics. 1994;22:336–339. PubMed

Kim UJ, Shizuya H, Sainz J, Garnes J, Pulst SM, deJong P, Simon MI. Construction and utility of a human chromosome 22-specific Fosmid library. Genet Anal Biomol Eng. 1995;12:81–84. PubMed

Kofler R, Bartoš J, Gong L, Stift G, Suchánková P, Šimková H, Berenyi M, Burg K, Doležel J, Lelley T. Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1. Theor Appl Genet. 2008;117:915–926. PubMed

Kooi MW, Aten JA, Stap J, Kipp JBA, Barendsen GW. Preparation of chromosome suspensions from cells of a solid experimental rumor for measurement by flow-cytometry. Cytometry. 1984;5:547–549. PubMed

Kopecký D, Číhalíková J, Kopecká J, Vrána J, Havránková M, Stočes Š, Bartoš J, Šimková H, Šafář J, Doležel J (2011) Establishing chromosome genomics in forage grasses. In: Abstracts of the “Eucarpia—29th Fodder Crops and Amenity Grasses Section Meeting”, Dublin, p 24

Korstanje R, Gillissen GF, den Bieman MG, Versteeg SA, van Oost B, Fox RR, van Lith HA, van Zutphen LFM. Mapping of rabbit chromosome 1 markers generated from a microsatellite-enriched chromosome-specific library. Anim Genet. 2001;32:308–312. PubMed

Kovářová P, Navrátilová A, Macas J, Doležel J. Chromosome analysis and sorting in Vicia sativa using flow cytometry. Biol Plant. 2007;51:43–48.

Krumlauf R, Jeanpierre M, Young BD. Construction and characterization of genomic libraries from specific human chromosomes. Proc Natl Acad Sci USA. 1982;79:2971–29758. PubMed PMC

Kubaláková M, Lysák MA, Vrána J, Šimková H, Číhalíková J, Doležel J. Rapid identification and determination of purity of flow-sorted plant chromosomes using C-PRINS. Cytometry. 2000;41:102–108. PubMed

Kubaláková M, Vrána J, Číhalíková J, Šimková H, Doležel J. Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.) Theor Appl Genet. 2002;104:1362–1372. PubMed

Kubaláková M, Valárik M, Bartoš J, Vrána J, Číhalíková J, Molnár-Láng M, Doležel J. Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. Genome. 2003;46:893–905. PubMed

Kubaláková M, Kovářová P, Suchánková P, Číhalíková J, Bartoš J, Lucretti S, Watanabe N, Kianian SF, Doležel J. Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics. 2005;170:823–829. PubMed PMC

Lan H, Shepel LA, Haag JD, Gould MN. Linkage mapping of rat chromosome 5 markers generated from chromosome-specific libraries. Mamm Genome. 1999;10:687–691. PubMed

Langer S, Kraus J, Jentsch I, Speicher MR. Multicolor chromosome painting in diagnostic and research applications. Chromosom Res. 2004;12:15–23. PubMed

Langford CF, Fischer PE, Binns MM, Holmes NG, Carter NP. Chromosome-specific paints from a high-resolution flow karyotype of the dog. Chromosom Res. 1996;4:115–123. PubMed

Langlois RG, Yu L-C, Gray JW, Carrano AV. Quantitative karyotyping of human chromosomes by dual beam flow cytometry. Proc Natl Acad Sci USA. 1982;79:7876–7880. PubMed PMC

Le Scouarnec S, Gribble SM. Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. Heredity. 2012;108:75–85. PubMed PMC

Lebo RV. Chromosome sorting and DNA sequence localization: a review. Cytometry. 1982;3:145–154. PubMed

Lebo RV, Gorin F, Fleterick RJ, Kao FT, Cheung MC, Bruce BD, Kan YW. High-resolution chromosome sorting and DNA spot-blot analysis assign McArdles syndrome to chromosome-11. Science. 1984;225:57–59. PubMed

Lebo RV, Golbus MS, Cheung MC. Detecting abnormal human-chromosome constitutions by dual laser flow cytogenetics. Am J Med Genet. 1986;25:519–529. PubMed

Lee JH, Arumuganathan K. Metaphase chromosome accumulation and flow karyotypes in rice (Oryza sativa L.) root tip meristem cells. Mol Cells. 1999;9:436–439. PubMed

Lee JY, Koi M, Stanbridge EJ, Oshimura M, Kumamoto AT, Feinberg AP. Simple purification of human-chromosomes to homogeneity using muntjac hybrid-cells. Nat Genet. 1994;7:29–33. PubMed

Lee JH, Arumuganathan K, Kaeppler SM, Papa CM, Kaeppler HF. Cell synchronization and isolation of metaphase chromosomes from maize (Zea mays L.) root tips for flow cytometric analysis and sorting. Genome. 1996;39:697–703. PubMed

Lee JH, Arumuganathan K, Yen Y, Kaeppler S, Kaeppler H, Baenziger PS. Root tip cell cycle synchronization and metaphase-chromosome isolation suitable for flow sorting in common wheat (Triticum aestivum L.) Genome. 1997;40:633–638. PubMed

Lee JH, Arumuganathan K, Chung YS, Kim KY, Chung WB, Bae KS, Kim DH, Chung DS, Kwon OC. Flow cytometric analysis and chromosome sorting of barley (Hordeum vulgare L.) Mol Cells. 2000;10:619–625. PubMed

Lee JH, Arumuganathan K, Kaeppler SM, Park SW, Kim KY, Chung YS, Kim DH, Fukui K. Variability of chromosomal DNA contents in maize (Zea mays L.) inbred and hybrid lines. Planta. 2002;215:666–671. PubMed

Leitch AR, Schwarzacher T, Wang ML, Leitch IJ, Surlan-Momirovich G, Moore G, Heslop-Harrison JS. Molecular cytogenetic analysis of repeated sequences in a long term wheat suspension culture. Plant Cell Tissue Organ Cult. 1993;33:287–296.

Levy HP, Schultz RA, Ordonez JV, Cohen MM. Anti-kinetochore staining for single laser, bivariate flow sorting of Indian muntjac chromosomes. Cytometry. 1991;12:695–700. PubMed

Li IJ, Arumuganathan K, Rines HW, Phillips RL, Riera-Lizarazu O, Sandhu D, Zhou Y, Gill KS. Flow cytometric sorting of maize chromosome 9 from an oat–maize chromosome addition line. Theor Appl Genet. 2001;102:658–663.

Li L, Arumuganathan K, Gill KS, Song Y. Flow sorting and microcloning of maize chromosome 1. Hereditas. 2004;141:55–60. PubMed

Lichten M, de Massy B. The impressionistic landscape of meiotic recombination. Cell. 2011;147:267–270. PubMed PMC

Lindenbaum M, Perkins E, Csonka E, Fleming E, Garcia L, Greene A, Gung L, Hadlaczky G, Lee E, Leung J, MacDonald N, Maxwell A, Mills K, Monteith D, Perez CF, Shellard J, Stewart S, Stodola T, Vandenborre D, Vanderbyl S, Ledebur HC. A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy. Nucleic Acids Res. 2004;32:172–186. PubMed PMC

Lucretti S, Doležel J. Bivariate flow karyotyping in broad bean (Vicia faba) Cytometry. 1997;28:236–242. PubMed

Lucretti S, Doležel J, Schubert I, Fuchs J. Flow karyotyping and sorting of Vicia faba chromosomes. Theor Appl Genet. 1993;85:665–672. PubMed

Luo MC, Thomas C, You FM, Hsiao J, Shu OY, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J. High-throughput fingerprinting of bacterial artificial chromosomes using the SNaPshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics. 2003;82:378–389. PubMed

Lysák MA, Číhalíková J, Kubaláková M, Šimková H, Künzel G, Doležel J. Flow karyotyping and sorting of mitotic chromosomes of barley (Hordeum vulgare L.) Chromosom Res. 1999;7:431–444. PubMed

Lysák MA, Fransz PF, Ali HBM, Schubert I. Chromosome painting in Arabidopsis thaliana. Plant J. 2001;28:689–697. PubMed

Ma RZ, Russ I, Park C, Heyen DW, Beever JE, Green CA, Lewin HA. Isolation and characterization of 45 polymorphic microsatellites from the bovine genome. Anim Genet. 1996;27:43–47. PubMed

Ma YZ, Lee JH, Li LC, Uchiyama S, Ohmido N, Fukui K. Fluorescent labeling of plant chromosomes in suspension by FISH. Gene Genet Syst. 2005;80:35–39. PubMed

Ma L, Xiao Y, Huang H, Wang QW, Rao WN, Feng Y, Zhang K, Song Q. Direct determination of molecular haplotypes by chromosome microdissection. Nat Methods. 2010;7:299–301. PubMed PMC

Macas J, Doležel J, Lucretti S, Pich U, Meister A, Fuchs J, Schubert I. Localization of seed protein genes on flow-sorted field bean chromosomes. Chromosom Res. 1993;1:107–115. PubMed

Macas J, Doležel J, Gualberti G, Pich U, Schubert I, Lucretti S. Primer-induced labelling of pea and field bean chromosomes in situ and in suspension. Biotechniques. 1995;19:402–408. PubMed

Macas J, Gualberti G, Nouzová M, Samec P, Lucretti S, Doležel J. Construction of chromosome-specific DNA libraries covering the whole genome of field bean (Vicia faba L.) Chromosom Res. 1996;4:531–539. PubMed

Macnab S, Whitehouse A. Progress and prospects: human artificial chromosomes. Gene Ther. 2009;16:1180–1188. PubMed

Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genom Hum Genet. 2008;9:387–402. PubMed

Margueron R, Reinberg D. Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet. 2010;11:285–296. PubMed PMC

Matsson P, Rydberg B. Analysis of chromosomes from human peripheral lymphocytes by flow cytometry. Cytometry. 1981;1:369–372. PubMed

Matsunaga S, Kawano S, Michimoto T, Higashiyama T, Nakao S, Sakai A, Kuroiwa T. Semi-automatic laser beam microdissection of the Y chromosome and analysis of Y chromosome DNA in a dioecious plant, Silene latifolia. Plant Cell Physiol. 1999;40:60–68. PubMed

Mayer KFX, Taudien S, Martis M, Šimková H, Suchánková P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, Scholz U, Graner A, Platzer M, Doležel J, Stein N. Gene content and virtual gene order of barley chromosome 1 H. Plant Physiol. 2009;151:496–505. PubMed PMC

Mayer KFX, Martis M, Hedley PE, Simkova H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubalakova M, Suchankova P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N. Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell. 2011;23:1249–1263. PubMed PMC

McCormick MK, Buckler A, Bruno W, Campbell E, Shera K, Torney D, Deaven L, Moyzis R. Construction and characterization of a YAC library with a low frequency of chimeric clones from flow-sorted human chromosome 9. Genomics. 1993;18:553–558. PubMed

McCormick MK, Campbell E, Deaven L, Moyzis R. Low-frequency chimeric yeast artificial chromosome libraries from flow-sorted human chromosomes 16 and 21. Proc Natl Acad Sci USA. 1993;90:1063–1067. PubMed PMC

Meksem K, Kahl G, editors. The handbook of plant genome mapping. Genetic and physical mapping. Weinheim: Wiley-VCH; 2005. pp. 151–171.

Metzker ML. Sequencing technologies—the next generation. Nat Rev Genet. 2010;11:31–46. PubMed

Miller JR, Dixon SC, Miller NGA, Tucker EM, Hindkjaer J, Thomsen PD. A chromosome-1-specific DNA library from the domestic pig (Sus scrofa domestica) Cytogenet Cell Genet. 1992;61:128–131. PubMed

Molnár I, Kubaláková M, Šimková H, Cseh A, Molnár-Láng M, Doležel J. Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata. PLoS One. 2011;6(11):e27708. PubMed PMC

Muñoz-Amatriaín M, Moscou MJ, Bhat PR, Svensson JT, Bartoš J, Suchánková P, Šimková H, Endo TR, Fenton RD, Lonardi S, Castillo AM, Chao S, Cistué L, Cuesta-Marcos A, Forrest KL, Hayden MJ, Hayes PM, Horsley RD, Makoto K, Moody D, Sato K, Vallés MP, Wulff BBH, Muehlbauer GJ, Doležel J, Close TJ. An improved consensus linkage map of barley based on flow-sorted chromosomes and single nucleotide polymorphism markers. Plant Genome. 2011;4:238–249.

Neely RK, Deen J, Hofkens J. Optical mapping of DNA: single-molecule-based methods for mapping genomes. Biopolymers. 2011;95:298–311. PubMed

Neumann P, Lysák M, Doležel J, Macas J. Isolation of chromosomes from Pisum sativum L. hairy root cultures and their analysis by flow cytometry. Plant Sci. 1998;137:205–215.

Neumann P, Požárková D, Vrána J, Doležel J, Macas J. Chromosome sorting and PCR-based physical mapping in pea (Pisum sativum L.) Chromosom Res. 2002;10:63–71. PubMed

Ng BL, Carter NP. Factors affecting flow karyotype resolution. Cytometry A. 2006;69:1028–1036. PubMed

Ng BL, Yang FY, Carter NP. Flow analysis and sorting of microchromosomes (< 3 Mb) Cytometry A. 2007;71:410–413. PubMed PMC

Nie W, O’Brien PCM, Ng BL, Fu B, Volobouev V, Carter NP, Ferguson-Smith MA, Yang F. Avian comparative genomics: reciprocal chromosome painting between domestic chicken (Gallus gallus) and the stone curlew (Burhinus oedicnemus, Charadriiformes)—an atypical species with low diploid number. Chromosom Res. 2009;17:99–113. PubMed PMC

Nie W, Wang J, Su W, Wang D, Tanomtong A, Perelman PL, Graphodatsky AS, Yang F. Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting. Heredity. 2012;108:17–27. PubMed PMC

Nizetic D, Gellen L, Hamvas R, Mott R, Grigoriev A, Vatcheva R, Zehetner G, Yaspo ML, Dutriau A, Lopes C, Delabar J-M, Van Broeckhoven C, Potler M-C, Lehrach H. An integrated YAC-overlap and “cosmid pocket” map of the human chromosome 21. Hum Mol Genet. 1994;3:759–770. PubMed

Nusse M, Viaggi S, Bonatti S. Identification and fate of a marker chromosome in methotrexate-resistant V79, B7 cells by flow karyotyping and sorting, metaphase analysis and in situ hybridization. Anal Cell Pathol. 1992;4:345–358. PubMed

Osman K, Higgins JD, Sanchez-Moran E, Armstrong SJ, Franklin FCH. Pathways to meiotic recombination in Arabidopsis thaliana. New Phytol. 2011;190:523–544. PubMed

Paux E, Roger D, Badaeva E, Gay G, Bernard M, Sourdille P, Feuillet C. Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J. 2006;48:463–474. PubMed

Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Bergès H, Eversole K, Appels R, Šafář J, Šimková H, Doležel J, Bernard M, Feuillet C. A physical map of the 1-gigabase bread wheat chromosome 3B. Science. 2008;322:101–104. PubMed

Pawlowski WP. Chromosome organization and dynamics in plants. Curr Opin Plant Biol. 2010;13:640–645. PubMed

Pich U, Meister A, Macas J, Doležel J, Lucretti S, Schubert I. Primed in situ labelling facilitates flow sorting of similar sized chromosomes. Plant J. 1995;7:1039–1044.

Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo W-L, Chen C, Zhai Y, Dairkee SH, Ljung B-M, Gray JW, Albertson DG. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998;20:207–211. PubMed

Požárková D, Koblížková A, Román B, Torres AM, Lucretti S, Lysák M, Doležel J, Macas J. Development and characterization of microsatellite markers from chromosome 1-specific DNA libraries of Vicia faba. Biol Plant. 2002;45:337–345.

Rens W, Vanoven CH, Stap J, Jakobs ME, Aten JA. Slit-scanning technique using standard cell sorter instruments for analyzing and sorting nonacrocentric human-chromosomes, including small ones. Cytometry. 1994;16:80–87. PubMed

Rommel B, Hutter KJ, Bullerdiek J, Barnitzke S, Goerttler K, Schloot W. Identification of flow-sorted chromosomes by G-banding and in situ hybridization. Cytometry. 1988;9:504–507. PubMed

Rubeš J, Pinton A, Bonnet-Garnier A, Fillon V, Musilová P, Michalová K, Kubíčková S, Ducos A, Yerle M. Fluorescence in situ hybridization applied to domestic animal cytogenetics. Cytogenet Genome Res. 2009;126:34–48. PubMed

Šafář J, Bartoš J, Janda J, Bellec A, Kubaláková M, Valárik M, Pateyron S, Weiserová J, Tušková R, Číhalíková J, Vrána J, Šimková H, Faivre-Rampant P, Sourdille P, Caboche M, Bernard M, Doležel J, Chalhoub B. Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J. 2004;39:960–968. PubMed

Šafář J, Šimková H, Kubaláková M, Číhalíková J, Suchánková P, Bartoš J, Doležel J. Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res. 2010;129:211–223. PubMed

Sankovic N, Delbridge ML, Grützner F, Ferguson-Smith MA, O’Brien PCM, Marshall Graves JA. Construction of a highly enriched marsupial Y chromosome-specific BAC sub-library using isolated Y chromosomes. Chromosom Res. 2006;14:657–664. PubMed

Sargan DR, Yang FT, Squire M, Milne BS, O’Brien PCM, Ferguson-Smith MA. Use of flow-sorted canine chromosomes in the assignment of canine linkage, radiation hybrid, and syntenic groups to chromosomes: refinement and verification of the comparative chromosome map for dog and human. Genomics. 2000;69:182–195. PubMed

Scalenghe F, Turco E, Ederström JE, Pirrotta V, Melli M. Microdissection and cloning of DNA from a specific region of Drosophila melanogaster polytene chromosomes. Chromosoma. 1981;82:205–216. PubMed

Scherthan H, Cremer T, Arnason U, Weier HU, Limadefaria A, Fronicke L. Comparative chromosome painting discloses homologous segments in distantly related mammals. Nat Genet. 1994;6:342–347. PubMed

Schmitz A, Oustry A, Chaput B, Bahridarwich I, Yerle M, Millan D, Frelat G, Cribiu EP. The bovine bivariate flow karyotype and peak identification by chromosome painting with PCR-generated probes. Mamm Genome. 1995;6:415–420. PubMed

Schondelmaier J, Martin R, Jahoor A, Houben A, Graner A, Koop HU, Herrmann RG, Jung C. Microdissection and microcloning of the barley (Hordeum vulgare L.) chromosome 1HS. Theor Appl Genet. 1993;86:629–636. PubMed

Schröck E, du Manoir S, Veldman T, Schoell B, Wienberg J, Ferguson-Smith MA, Ning Y, Ledbetter DH, Bar-Am I, Soenksen D, Garini Y, Ried T. Multicolor spectral karyotyping of human chromosomes. Science. 1996;273:494–497. PubMed

Schubert I, Oud JL. There is an upper limit of chromosome size for normal development of an organism. Cell. 1997;88:515–520. PubMed

Schubert I, Doležel J, Houben A, Scherthan H, Wanner G. Refined examination of plant metaphase chromosome structure at different levels made feasible by new isolation methods. Chromosoma. 1993;102:96–101.

Schubert I, Fransz PF, Fuchs J, de Jong JH. Chromosome painting in plants. Methods Cell Sci. 2001;23:57–69. PubMed

Schwarzacher T, Wang ML, Leitch AR, Miller N, Moore G, Heslop-Harrison JS. Flow cytometric analysis of the chromosomes and stability of a wheat cell-culture line. Theor Appl Genet. 1997;94:91–97. PubMed

Shepel LA, Morrissey LW, Hsu LC, Gould MN. Bivariate flow karyotyping, sorting, and peak assignment of all rat chromosomes. Genomics. 1994;19:75–85. PubMed

Shepel LA, Lan H, Brasic GM, Gheen ME, Hsu LC, Haag JD, Gould MN. Mapping of 55 new rat microsatellite markers from chromosome-specific libraries. Mamm Genome. 1998;9:622–628. PubMed

Sillar R, Young BD. A new method for the preparation of metaphase chromosomes for flow analysis. J Histochem Cytochem. 1981;29:74–78. PubMed

Silverman GA, Schneider SS, Massa HF, Flint A, Lalande M, Leonard JC, Overhauser J, van den Engh G, Trask BJ. The 18Q(−) syndrome—analysis of chromosomes by bivariate flow karyotyping and the PCR reveals a successive set of deletion breakpoints within 18Q21.2–Q22.2. Am J Hum Genet. 1995;56:926–937. PubMed PMC

Šimková H, Šafář J, Suchánková P, Kovářová P, Bartoš J, Kubaláková M, Janda J, Číhalíková J, Mago R, Lelley T, Doležel J. A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS) BMC Genomics. 2008;9:237. PubMed PMC

Speicher MR, Gwyn Ballard S, Ward DC. Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet. 1996;12:368–375. PubMed

Stallings RL, Torney DC, Hildebrand CE, Longmire JL, Deaven LL, Jett JH, Doggett NA, Moyzis RK. Physical mapping of human chromosomes by repetitive sequence fingerprinting. Proc Natl Acad Sci USA. 1990;87:6218–6222. PubMed PMC

Stepanov SI, Konyshev VN, Kotlovanova LV, Roganov AP. Karyotyping of individual cells with flow cytometry. Cytometry. 1996;23:279–283. PubMed

Stubblefield E, Oro J. The isolation of specific chicken macrochromosomes by zonal centrifugation and flow sorting. Cytometry. 1982;5:73–281. PubMed

Stubblefield E, Cram S, Deaven L. Flow microfluorometric analysis of isolated Chinese-hamster chromosomes. Exp Cell Res. 1975;94:464–468. PubMed

Suchánková P, Kubaláková M, Kovářová P, Bartoš J, Číhalíková J, Molnár-Láng M, Endo TR, Doležel J. Dissection of the nuclear genome of barley by chromosome flow sorting. Theor Appl Genet. 2006;113:651–659. PubMed

Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, Lynch D, Teboul L, Brown SD, Li H, Ning Z, Nadeau JH, Croniger CM, Durbin R, Adams DJ. Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biol. 2009;10:112. PubMed PMC

Szinay D, Bai Y, Visser R, de Jong H. FISH applications for genomics and plant breeding strategies in tomato and other solanaceous crops. Cytogenet Genome Res. 2010;129:199–210. PubMed

Takata H, Uchiyama S, Nakamura N, Nakashima S, Kobayashi S, Sone T, Kimura S, Lahmers S, Granzier H, Labeit S, Matsunaga S, Fukui K. A comparative proteome analysis of human metaphase chromosomes isolated from two different cell lines reveals a set of conserved chromosome-associated proteins. Gene Cell. 2007;12:269–284. PubMed

Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou SG, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM, Kohn S, Runnheim R, Lamers C, Forrest D, Newton MA, Eichler EE, Kent-First M, Surti U, Livny M, Schwartz DC. High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci USA. 2010;107:10848–10853. PubMed PMC

Telenius H, Pelmear AH, Tunnacliffe A, Carter NP, Behmel A, Ferguson-Smith MA, Nordenskjöld M, Pfragner R, Ponder BA. Cytogenetic analysis by chromosome painting using DOP-PCR amplified flow-sorted chromosomes. Gene Chromosome Cancer. 1992;4:257–263. PubMed

Telenius H, Devos D, Blennow E, Willat LR, Ponder BAJ, Carter NP. Chromatid contamination can impair the purity of flow-sorted metaphase chromosomes. Cytometry. 1993;14:97–101. PubMed

ten Hoopen R, Manteuffel R, Doležel J, Malysheva L, Schubert I. Evolutionary conservation of kinetochore protein sequences in plants. Chromosoma. 2000;109:482–489. PubMed

Trask BJ, van den Engh G, Gray J, van der Laan M, Turner B. Immunofluorescent detection of histone-2B on metaphase chromosomes using flow-cytometry. Chromosoma. 1984;90:295–302. PubMed

Trask BJ, Van den Engh G, Landegent J, In de Wal NJ, Van der Ploegh M. Detection of DNA sequences in nuclei in suspension by in situ hybridization and dual beam flow cytometry. Science. 1985;230:1401–1403. PubMed

Trask BJ, Mefford H, van den Engh G, Massa HF, Juyal RC, Potocki L, Finucane B, Abuelo DN, Witt DR, Magenis E, Baldini A, Greenberg F, Lupski JR, Patel PI. Quantification by flow cytometry of chromosome-17 deletions in Smith–Magenis syndrome patients. Hum Genet. 1996;98:710–718. PubMed

Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2012;13:36–46. PubMed PMC

Überall I, Vrána J, Bartoš J, Šmerda J, Doležel J, Havel L. Isolation of chromosomes from Picea abies L. and their analysis by flow cytometry. Biol Plant. 2004;48:199–203.

Uchiyama S, Kobayashi S, Takata H, Ishihara T, Hori N, Higashi T, Hayashihara K, Sone T, Higo D, Nirasawa T, Takao T, Matsunaga S, Fukui K. Proteome analysis of human metaphase chromosomes. J Biol Chem. 2005;280:16994–17004. PubMed

Valárik M, Bartoš J, Kovářová P, Kubaláková M, de Jong H, Doležel J. High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J. 2004;37:940–950. PubMed

van den Engh G, Trask B, Cram S, Bartholdi M. Preparation of chromosome suspensions for flow-cytometry. Cytometry. 1984;5:108–117. PubMed

Van Dilla MA, Deaven LL. Construction of gene libraries for each human chromosome. Cytometry. 1990;11:208–218. PubMed

Van Dilla MA, Deaven LL, Albright KL, Allen NA, Aubuchon MR, Bartholdi MF, Browne NC, Campbell EW, Carrano AV, Clark LM, Cram LS, Fuscoe JC, Gray JW, Hildebrand CE, Jackson PJ, Jett JH, Longmire JL, Lozes CR, Luedemann ML, Martin JC, McNinch JS, Meincke LJ, Mendelsohn ML, Meyne J, Moyzis RK, Munk AC, Perlman J, Peters DC, Silva AJ, Trask BJ. Human chromosome-specific DNA libraries: construction and availability. Biotechnology. 1986;4:537–552.

Van Devanter DR, Choongkittaworn NM, Dyer KA, Aten J, Otto P, Behler C, Bryant EM, Rabinovitch PS. Pure chromosome-specific PCR libraries from single sorted chromosomes. Proc Natl Acad Sci USA. 1994;91:5858–5862. PubMed PMC

Veltman IM, Veltman JA, Arkesteijn G, Janssen IM, Vissers LE, de Jong PJ, van Kessel AG, Schoenmakers EF. Chromosomal breakpoint mapping by arrayCGH using flow-sorted chromosomes. Biotechniques. 2003;35:1066–1070. PubMed

Verdaasdonk JS, Bloom K. Centromeres: unique chromatin structures that drive chromosome segregation. Nat Rev Mol Cell Biol. 2011;12:320–332. PubMed PMC

Veuskens J, Marie D, Brown SC, Jacobs M, Negrutiu I. Flow sorting of the Y sex chromosome in the dioecious plant Melandrium album. Cytometry. 1995;21:363–373. PubMed

Vitharana SN, Wilson GS. Fractionation of chromosome 15 with an affinity-based approach using magnetic beads. Genomics. 2006;87:158–164. PubMed

Vitulo N, Albiero A, Forcato C, Campagna D, Dal Pero F, Bagnaresi P, Colaiacovo M, Faccioli P, Lamontanara A, Šimková H, Kubaláková M, Perrotta G, Facella P, Lopez L, Pietrella M, Gianese G, Doležel J, Giuliano G, Cattivelli L, Valle G, Stanca AM. First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One. 2011;6:e26421. PubMed PMC

Vláčilová K, Ohri D, Vrána J, Číhalíková J, Kubaláková M, Kahl G, Doležel J. Development of flow cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.) Chromosom Res. 2002;10:695–706. PubMed

Vooijs M, Yu LC, Tkachuk D, Pinkel D, Johnson D, Gray JW. Libraries for each human-chromosome, constructed from sorter-enriched chromosomes by using linker-adapter PCR. Am J Hum Genet. 1993;52:586–597. PubMed PMC

Vrána J, Kubaláková M, Šimková H, Číhalíková J, Lysák MA, Doležel J. Flow-sorting of mitotic chromosomes in common wheat (Triticum aestivum L.) Genetics. 2000;156:2033–2041. PubMed PMC

Wang ML, Leitch AR, Schwarzacher T, Heslop-Harrison JS, Moore G. Construction of a chromosome-enriched HpaII library from flow-sorted wheat chromosomes. Nucleic Acids Res. 1992;20:1897–1901. PubMed PMC

Wanner G, Formanek H, Martin R, Herrmann RG. High resolution scanning electron microscopy of plant chromosomes. Chromosoma. 1991;100:103–109.

Wei FS, Zhang JW, Zhou SG, He RF, Schaeffer M, Collura K, Kudrna D, Faga BP, Wissotski M, Golser W, Rock SM, Graves TA, Fulton RS, Coe E, Schnable PS, Schwartz DC, Ware D, Clifton SW, Wilson RK, Wing RA. The physical and genetic framework of the maize B73 genome. PLoS Genet. 2009;5:e1000715. PubMed PMC

Wenzl P, Suchánková P, Carling J, Šimková H, Huttner E, Kubaláková M, Sourdille P, Paul E, Feuillet C, Kilian A, Doležel J. Isolated chromosomes as a new and efficient source of DArT markers for the saturation of genetic maps. Theor Appl Genet. 2010;121:465–474. PubMed

Wicker T, Mayer KFX, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Doležel J, Keller B, Stein N. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell. 2011;23:1706–1718. PubMed PMC

Wlodkowic D, Darzynkiewicz Z (2011) Rise of the micromachines: microfluidics and the future of cytometry. In: Darzynkiewicz Z, Holden E, Orfao A, Telford W., Wlodkowic (eds) Methods in cell biology, vol 102. Recent advances in cytometry, part A: instrumentation, methods. Academic Press, San Diego, pp 105–125 PubMed PMC

Yang H, Chen X, Wong WH. Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci USA. 2011;108:12–17. PubMed PMC

Yanowitz J. Meiosis: making a break for it. Curr Opin Cell Biol. 2010;22:744–751. PubMed PMC

Yerle M, Schmitz A, Milan D, Chaput B, Monteagudo L, Vaiman M, Frelat G, Gellin J. Accurate characterization of porcine bivariate flow karyotype by PCR and fluorescence in situ hybridization. Genomics. 1993;16:97–103. PubMed

Young BD, Ferguson-Smith MA, Sillar R, Boyd E. High-resolution analysis of human peripheral lymphocyte chromosomes by flow-cytometry. Proc Natl Acad Sci USA. 1981;78:7727–7731. PubMed PMC

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O’Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011;480:520–524. PubMed PMC

Zatloukalová P, Hřibová E, Kubaláková M, Suchánková P, Šimková H, Adoración C, Kahl G, Millán T, Doležel J. Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes. Chromosom Res. 2011;19:729–739. PubMed

Zhou SG, Wei FS, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC. A single molecule scaffold for the maize genome. PLoS Genet. 2009;5:e1000711. PubMed PMC

Zhou VW, Goren A, Bernstein BE. Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet. 2011;12:7–18. PubMed

Barley MLA3 recognizes the host-specificity effector Pwl2 from Magnaporthe oryzae

Comparative genomic analysis of 5Mg chromosome of Aegilops geniculata and 5Uu chromosome of Aegilops umbellulata reveal genic diversity in the tertiary gene pool

Flow Cytometric Analysis and Sorting of Plant Chromosomes

Flow karyotyping of wheat-Aegilops additions facilitate dissecting the genomes of Ae. biuncialis and Ae. geniculata into individual chromosomes

Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale

A lineage-specific Exo70 is required for receptor kinase-mediated immunity in barley

Proteome Analysis of Condensed Barley Mitotic Chromosomes

Chromosome analysis and sorting

A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Identification of a Dominant Chlorosis Phenotype Through a Forward Screen of the Triticum turgidum cv. Kronos TILLING Population

Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

Guidelines for the use of flow cytometry and cell sorting in immunological studies

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

Development of intron targeting (IT) markers specific for chromosome arm 4VS of Haynaldia villosa by chromosome sorting and next-generation sequencing

The Enigma of Progressively Partial Endoreplication: New Insights Provided by Flow Cytometry and Next-Generation Sequencing

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Flow sorting of C-genome chromosomes from wild relatives of wheat Aegilops markgrafii, Ae. triuncialis and Ae. cylindrica, and their molecular organization

Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene

Efficient high-throughput sequencing of a laser microdissected chromosome arm