Skip to main content
SpringerLink
Log in

Assembly of the Flax Genome into Chromosomes

  • Chapter
  • First Online:
Genetics and Genomics of Linum

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 23))

Abstract

Flax (Linum usitatissimum L.) is a diploid species with a haploid number of 15 chromosomes. The flax genome has been sequenced, and the first draft reference sequence was released in 2012. Flax genomic resources including bacterial artificial chromosome (BAC) libraries, a BAC-based physical map, BAC-end sequences, high-density genetic maps, and a BioNano genome optical map have been developed. Integration of these genomic resources assisted in the validation the draft reference sequence and its ordering into chromosomes, resulting in a higher-quality flax reference sequence useful for genome evolution studies, comparative genomic analyses, genetic research and molecular breeding.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB (2013) Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science 342:1516–1517

    Article  CAS  Google Scholar 

  • Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537–545

    Article  Google Scholar 

  • Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer E, Walichnowski A, Ward K, Rowland G, Duguid S, Banik M (2012) Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). Theor Appl Genet 125:1783–1795

    Article  Google Scholar 

  • Cullis CA (1981) DNA sequence organization in the flax genome. Biochim Biophys Acta 652:1–15

    Article  CAS  Google Scholar 

  • Dolezel J, Greilhuber J, Suda J (2007) Estimation of nuclear DNA content in plants using flow cytometry. Nat Protoc 2:2233–2244

    Article  CAS  Google Scholar 

  • Evans GM, Rees H, Snell CL, Sun S (1972) The relationship between nuclear DNA amount and the duration of the mitotic cycle. Chromosomes Today 3:24–31

    CAS  Google Scholar 

  • Fu YB, Dong Y, Yang MH (2016) Multiplexed shotgun sequencing reveals congruent three-genome phylogenetic signals for four botanical sections of the flax genus Linum. Mol Phylogenet Evol 101:122–132

    Article  Google Scholar 

  • Goldblatt P (2007) The index to plant chromosome numbers: past and future. Taxon 56:984–986

    Article  Google Scholar 

  • Marie D, Brown SC (1993) A cytometric exercise in plant DNA histograms, with 2C values for 70 species. Biol Cell 78:41–51

    Article  CAS  Google Scholar 

  • McDill J, Repplinger M, Simpson BB, Kadereit JW (2009) The phylogeny of Linum and Linaceae subfamily Linoideae, with implications for their systematics, biogeography, and evolution of heterostyly. Syst Bot 34:386–405

    Article  Google Scholar 

  • Muravenko OV, Samatadze TE, Popov KV, Amosova AV, Zelenin AV (2001) Comparative genome analysis in two flax species by C-banding patterns. Russ J Genet 37:253–256

    Article  CAS  Google Scholar 

  • Muravenko OV, Lemesh VA, Samatadze TE, Amosova AV, Grushetskaia ZE, Popov KV, Semenova O, Khotyleva LV, Zelenin AV (2003) Genome comparisons of three closely related flax species and their hybrids with chromosomal and molecular markers. Genetika 39:510–518

    CAS  PubMed  Google Scholar 

  • Nosova IV (2005) A study of the Linum species, Sect. Syllinum and Dasylinum. In: Karyology, karyosystematics and molecular phylogeny, pp 73–74, St. Petersburg, Russia.

    Google Scholar 

  • Nosova IV, Yu Semenova O, Samatadze TE, Amosova AV, Bolsheva NL, Zelenin AV, Muravenko OV (2005) Investigation of karyotype structure and mapping of ribosomal genes on chromosomes of wild Linum species by FISH. Biol Membr 22:244–248

    CAS  Google Scholar 

  • Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annu Rev Genet 34:401–437

    Article  CAS  Google Scholar 

  • Ragupathy R, Rathinavelu R, Cloutier S (2011) Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. BMC Genomics 12:217

    Article  CAS  Google Scholar 

  • Ray C (1944) Cytological studies on the flax genus, Linum. Am J Bot 31:241–248

    Article  Google Scholar 

  • Rice A, Glick L, Abadi S, Einhorn M, Kopelman NM, Salman-Minkov A, Mayzel J, Chay O, Mayrose I (2014) The chromosome counts database (CCDB) – a community resource of plant chromosome numbers. New Phytol 206:19–26

    Article  Google Scholar 

  • Rogers CM (1982) The systematics of Linum sect. Linopsis (Linaceae). Plant Syst Evol 140:225–234

    Article  Google Scholar 

  • Rowland GG, Hormis YA, Rashid KY (2002) CDC Bethune flax. Can J Plant Sci 82:101–102

    Article  Google Scholar 

  • Shearer LA, Anderson LK, de Jong H, Smit S, Goicoechea JL, Roe BA, Hua A, Giovannoni JJ, Stack SM (2014) Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome. G3 (Bethesda) 4:1395–1405

    Article  CAS  Google Scholar 

  • Stankova H, Hastie AR, Chan S, Vrana J, Tulpova Z, Kubalakova M, Visendi P, Hayashi S, Luo M, Batley J, Edwards D, Dolezel J, Simkova H (2016) BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnol J 14:1523–1531

    Article  CAS  Google Scholar 

  • Sveinsson S, McDill J, Wong GKS, Li J, Li X, Deyholos MK, Cronk QCB (2014) Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics. Ann Bot 113:753–761

    Article  Google Scholar 

  • Venter JC, Smith HO, Hood L (1996) A new strategy for genome sequencing. Nature 381:364–366

    Article  CAS  Google Scholar 

  • Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GK, Wang J, Deyholos MK (2012) The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 72:461–473

    Article  Google Scholar 

  • You FM, Li P, Ragupathy R, Kumar S, Zhu T, Luo M-C, Duguid SD, Rashid KY, Booker HM, Deyholos MK, Fu YB, Sharpe AG, Cloutier S (2016) The draft flax genome pseudomolecules. In: The 66th Flax Institute of the United States, Fargo, North Dakota, USA, pp 17–24

    Google Scholar 

  • You FM, Xiao J, Li P, Yao Z, Jia G, He L, Zhu T, Luo M-C, Wang X, Deyholos MK, Cloutier S (2018) Chromosome-scale pseudomolecules refined by optical, physical, and genetic maps in flax. Plant J 95:371–384. https://doi.org/10.1111/tpj.13944

    Article  CAS  PubMed  Google Scholar 

  • Young ND, Debelle 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, Berges 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, Gonzalez AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jocker 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, Denarie J, Dixon RA, May GD, Schwartz DC, Rogers J, Quetier F, Town CD, Roe BA (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524

    Article  CAS  Google Scholar 

  • Zhou S, Wei F, 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 (2009) A single molecule scaffold for the maize genome. PLoS Genet 5:e1000711

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada

    Frank M. You

Authors
  1. Frank M. You
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sylvie Cloutier
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Frank M. You .

Editor information

Editors and Affiliations

  1. Department of Biology, Case Western Reserve University, Cleveland, OH, USA

    Christopher A. Cullis

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

You, F.M., Cloutier, S. (2019). Assembly of the Flax Genome into Chromosomes. In: Cullis, C. (eds) Genetics and Genomics of Linum. Plant Genetics and Genomics: Crops and Models, vol 23. Springer, Cham. https://doi.org/10.1007/978-3-030-23964-0_5

Download citation

Publish with us

Policies and ethics

Search

Navigation