Skip to main content
SpringerLink
Log in
Book cover

The Barley Genome pp 123–138Cite as

The Repetitive Landscape of the Barley Genome

  • Chapter
  • First Online:

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

While transposable elements (TEs) comprise the bulk of plant genomic DNA, how they contribute to genome structure and organization is still poorly understood. Especially, in large genomes where TEs make the majority of genomic DNA, it is still unclear whether TEs target specific chromosomal regions or whether they simply accumulate where they are best tolerated. The barley genome with its vast repetitive fraction is an ideal system to study chromosomal organization and evolution of TEs. Genes make only about 2% of the genome, while over 80% is derived from TEs. The TE fraction is composed of at least 350 different families. However, 50% of the genome is comprised of only 15 high-copy TE families, while all other TE families are present in moderate or low-copy numbers. The barley genome is highly compartmentalized with different types of TEs occupying different chromosomal “niches”, such as distal, interstitial or proximal regions of chromosome arms. Furthermore, gene space represents its own distinct genomic compartment that is enriched in small non-autonomous DNA transposons, suggesting that these TEs specifically target promoters and downstream regions. Some TE families also show a strong preference to insert in specific sequence motifs which may, in part, explain their distribution. The family-specific distribution patterns result in distinct TE compositions of different chromosomal compartments.

This is a preview of subscription content, 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   139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   249.99
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

Learn about institutional subscriptions

References

  • Abe H, Gemmell NJ (2014) Abundance, arrangement, and function of sequence motifs in the chicken promoters. BMC Genom 15:900

    Article  CAS  Google Scholar 

  • Buchmann JP, Matsumoto T, Stein N, Keller B, Wicker T (2012) Interspecies sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity. Plant J 488:213–217

    Google Scholar 

  • Buchmann JP, Löytynoja A, Wicker T, Schulman AH (2014) Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts. MobDNA 5(1):24. https://doi.org/10.1186/1759-8753-5-24

  • Bureau T, Wessler SR (1994a) Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc Natl Acad Sci USA 9:1411–1415

    Google Scholar 

  • Bureau T, Wessler SR (1994b) Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Proc Natl Acad Sci USA 9:907–916

    Google Scholar 

  • Chalopin D, Naville M, Plard F, Galiana D, Volff JN (2015) Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol 7:567–580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chang W, Schulman AH (2008) BARE retrotransposons produce multiple groups of rarely polyadenylated transcripts from two differentially regulated promoters. Plant J 56:40–50

    Article  CAS  PubMed  Google Scholar 

  • Chang W et al (2013) BARE Retrotransposons are translated and replicated via distinct RNA pools. PLoS ONE 8:e72270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • d’Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–217

    Article  CAS  PubMed  Google Scholar 

  • Gladyshev EA, Arkhipova IR (2011) A widespread class of reverse transcriptase-related cellular genes. Proc Natl Acad Sci USA 108:20311–20316

    Article  PubMed  Google Scholar 

  • Han Y, Qin S, Wessler SR (2013) Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes. BMC Genom 14:71

    Article  CAS  Google Scholar 

  • Hirsch CD, Springer NM (2016) Transposable element influences on gene expression in plants. Biochim Biophys Acta S1874–9399:30100–30106

    Google Scholar 

  • Hudakova S, Michalek W, Presting GG, ten Hoopen R, dos Santos K, Jasencakova Z, Schubert I (2001) Sequence organization of barley centromeres. Nucleic Acids Res 29:5029–5035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768

    Article  CAS  Google Scholar 

  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Google Scholar 

  • Jääskeläinen M et al (1999) Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells. Plant J 20:413–422

    Article  PubMed  Google Scholar 

  • Jääskeläinen M et al (2013) Retrotransposon BARE displays strong tissue-specific differences in expression. New Phytol 200:1000–1008

    Article  CAS  PubMed  Google Scholar 

  • Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, Schulman AH (2004) LARD retroelements: novel, non-autonomous components of barley and related genomes. Genetics 166:1437–1450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kapitonov VV, Jurka J (2007) Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 23:521–529

    Article  CAS  PubMed  Google Scholar 

  • Kelly LJ, Renny-Byfield S, Pellicer J, Macas J, Novák P, Neumann P et al (2015) Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. New Phytol 208:596–607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kempken F, Windhofer F (2001) The hAT family: a versatile transposon group common to plants, fungi, animals, and man. Chromosoma 110:1–9

    Article  CAS  PubMed  Google Scholar 

  • Leitch IJ, Beaulieu JM, Cheung K, Hanson L, Lysak MA, Fay MF (2007) Punctuated genome size evolution in Liliaceae. J Evol Biol 20:2296–2308

    Article  CAS  PubMed  Google Scholar 

  • Leushkin EV, Sutormin RA, Nabieva ER, Penin AA, Kondrashov AS, Logacheva MD (2013) The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences. BMC Genom 14:476

    Article  CAS  Google Scholar 

  • Malik HS, Eickbush TH (2001) Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res 11:1187–1197

    Article  CAS  PubMed  Google Scholar 

  • Manninen I, Schulman AH (1993) BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol Biol 22:829–846

    Article  CAS  PubMed  Google Scholar 

  • Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T et al (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544:427–433

    Article  CAS  PubMed  Google Scholar 

  • Middleton CP, Stein N, Keller B, Kilian B, Wicker T (2012) Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity. Plant J. 73:347–356

    Article  CAS  PubMed  Google Scholar 

  • Neumann P, Navrátilová A, Koblížková A, Kejnovský E, Hřibová E, Hobza R, Widmer A, Doležel J, Macas J (2011) Plant centromeric retrotransposons: a structural and cytogenetic perspective. Mob DNA. 2:4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556. https://doi.org/10.1038/nature07723

  • Roffler S, Wicker T (2015) Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons. Mob DNA. 6:8

    Article  PubMed  PubMed Central  Google Scholar 

  • Sabot F, Schulman AH (2006) Parasitism and the retrotransposon life cycle in plants: a hitchhiker’s guide to the genome. Heredity 97:381–388

    Article  CAS  PubMed  Google Scholar 

  • Sabot F, Sourdille P, Chantret N, Bernard M (2006) Morgane, a new LTR retrotransposon group, and its subfamilies in wheats. Genetica 128:439–447

    Article  CAS  PubMed  Google Scholar 

  • Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115. https://doi.org/10.1126/science.1178534

  • Schulman AH (2013) Retrotransposon replication in plants. Curr Opin Virol 3:604–614

    Article  CAS  PubMed  Google Scholar 

  • Suoniemi A et al (1996) The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol Biol 31:295–306

    Article  CAS  PubMed  Google Scholar 

  • Tanskanen JA et al (2007) Life without GAG: The BARE-2 retrotransposon as a parasite’s parasite. Gene 390:166–174

    Article  CAS  PubMed  Google Scholar 

  • Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH (1999) Retrotransposon BARE-1 and Its role in genome evolution in the genus Hordeum. Plant Cell 11:1769–1784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wicker T, Guyot R, Yahiaoui N, Keller B (2003) CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements. Plant Physiol 132:52–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982

    Article  CAS  PubMed  Google Scholar 

  • Wicker T, Yu Y, Haberer G, Mayer KFX, Marri PR, Rounsley S et al (2016) DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nat Commun 7:12790

    Article  PubMed  PubMed Central  Google Scholar 

  • Wicker T, Schulman AH, Tanskanen J, Spannagl M, Twardziok S, Mascher M, Springer NM, Li Q, Waugh R, Li C, Zhang G, Stein N, Mayer KFX, Gundlach H (2017) The repetitive landscape of the 5,100 Mbp barley genome, Mob. DNA 8:22

    Google Scholar 

  • Yang L, Bennetzen JL (2009) Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci USA 106:19922–19927

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland

    Thomas Wicker

  2. PGSB—Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany

    Heidrun Gundlach

  3. Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland

    Alan H. Schulman

  4. Green Technology, Natural Resources Institute Finland (Luke), Helsinki, Finland

    Alan H. Schulman

Authors
  1. Thomas Wicker
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Heidrun Gundlach
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alan H. Schulman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Thomas Wicker .

Editor information

Editors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Sachsen-Anhalt, Germany

    Nils Stein

  2. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA

    Gary J. Muehlbauer

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Wicker, T., Gundlach, H., Schulman, A.H. (2018). The Repetitive Landscape of the Barley Genome. In: Stein, N., Muehlbauer, G. (eds) The Barley Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-92528-8_9

Download citation

Publish with us

Policies and ethics

Search

Navigation