Skip to main content
SpringerLink
Log in

Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content

  • Chapter
  • First Online:
Plant Transposable Elements

Part of the book series: Topics in Current Genetics ((TCG,volume 24))

Abstract

Transposable element (TE) content explains a large part of Eukaryotic genome size variation. TE content is determined by transposition, removal and host responses, but the efficiency of these forces is ultimately governed by genetic drift and natural selection. Contribution of TE families to genome size variation has been recently quantified using next generation sequencing (NGS) in two species pairs: Zea mays ssp. mays and Zea luxurians, Arabidopsis lyrata and A. thaliana. In both interspecific comparisons, genome-wide differences in TE content rather than the proliferation of a small subset of TE families was observed. We discuss three nonexclusive hypotheses to explain this pattern: selection for genome shrinkage, differential efficiency of epigenetic control, and a purely stochastic process of genome size evolution. Additional genome-wide assessments are needed to assess the extent to which selection shapes TE genomic content. To facilitate such studies, we discuss the use of NGS in “orphan” species.

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 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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

  • Almeida R, Allshire R (2005) RNA silencing and genome regulation. Trends Cell Biol 15:251–258

    Article  PubMed  CAS  Google Scholar 

  • Ananiev EV, Phillips RL, Rines HW (1998) A knob-associated repeat in maize capable of forming fold-back DNA segments: Are chromosome knobs megatransposons? Proc Natl Acad Sci USA 95:10785–10790

    Article  PubMed  CAS  Google Scholar 

  • Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J, Anthouard V, Scarpelli C, Artiguenave F, Wincker P (2008) High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics 9:603

    Article  PubMed  Google Scholar 

  • Baucom R, Estill J, Chaparro C, Upshaw N, Jogi A, Deragon J, Westerman R, Sanmiguel P, Bennetzen J (2009) Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet 5:e1000732

    Article  PubMed  Google Scholar 

  • Bedell JA, Korf I, Gish W (2000) MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 16:1040–1041

    Article  PubMed  CAS  Google Scholar 

  • Bennett MD, Leitch IJ, Hanson L (1998) DNA amounts in two samples of angiosperm weeds. Ann Bot 82:121–134

    Article  Google Scholar 

  • Biemont C (2008) Genome size evolution: within-species variation in genome size. Heredity 101:297–298

    Article  PubMed  CAS  Google Scholar 

  • Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A (2005) Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17:343–360

    Article  PubMed  CAS  Google Scholar 

  • Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Muller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:956–960

    Article  PubMed  CAS  Google Scholar 

  • Chevin LM, Hospital F (2008) Selective sweep at a quantitative trait locus in the presence of background genetic variation. Genetics 180:1645–1660

    Article  PubMed  Google Scholar 

  • DeBarry JD, Liu R, Bennetzen JL (2008) Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics 9:235

    Article  PubMed  Google Scholar 

  • Devos KM, Brown JK, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12:1075–1079

    Article  PubMed  CAS  Google Scholar 

  • Diao XM, Freeling M, Lisch D (2006) Horizontal transfer of a plant transposon. PLoS Biol 4:119–128

    Article  CAS  Google Scholar 

  • Fawcett JA, Rouzé P, Van de Peer Y (2011) Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. Mol Biol Evol 29:849–859

    Article  PubMed  Google Scholar 

  • Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Basturkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D’Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Penalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438:1105–1115

    Article  PubMed  CAS  Google Scholar 

  • Gaut B, Ross-Ibarra J (2008) Selection on major components of angiosperm genomes. Science 320:484–486

    Article  PubMed  CAS  Google Scholar 

  • Gaut B, Le Thierry d’Ennequin M, Peek A, Sawkins M (2000) Maize as a model for the evolution of plant nuclear genomes. Proc Natl Acad Sci USA 97:7008–7015

    Article  PubMed  CAS  Google Scholar 

  • Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 108:1513–1518

    Article  PubMed  CAS  Google Scholar 

  • Gonzalez GE, Poggio L (2011) Karyotype of Zea luxurians and Z. mays subsp mays using FISH/DAPI, and analysis of meiotic behavior of hybrids. Genome 54:26–32

    Article  PubMed  CAS  Google Scholar 

  • Gossmann TI, Song BH, Windsor AJ, Mitchell-Olds T, Dixon CJ, Kapralov MV, Filatov DA, Eyre-Walker A (2010) Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Mol Biol Evol 27:1822–1832

    Article  PubMed  CAS  Google Scholar 

  • Grotkopp E, Rejmanek M, Sanderson MJ, Rost TL (2004) Evolution of genome size in pines (Pinus) and its life-history correlates: supertree analyses. Evolution 58:1705–1729

    PubMed  CAS  Google Scholar 

  • Guillin EA, Poggio L, Naranjo CA (1992) Genome size in annual species of Zea. Relation with cellular parameters and altitude. Maize Genet Coop Newslett 66:59–60

    Google Scholar 

  • Hanson M, Gaut B, Stec A, Fuerstenberg S, Goodman M, Coe E, Doebley J (1996) Evolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci. Genetics 143:1395–1407

    PubMed  CAS  Google Scholar 

  • Hawkins J, Kim H, Nason J, Wing R, Wendel J (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16:1252–1261

    Article  PubMed  CAS  Google Scholar 

  • Hollister J, Gaut B (2009) Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res 19:1419–1428

    Article  PubMed  CAS  Google Scholar 

  • Hollister J, Smith L, Ott F, Guo Y-L, Weigel D, Gaut B (2011) Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci USA 108:2322–2327

    Article  PubMed  CAS  Google Scholar 

  • Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 43:476–481

    Article  PubMed  Google Scholar 

  • Initiative TAG (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Knight CA, Molinari NA, Petrov DA (2005) The large genome constraint hypothesis: evolution, ecology and phenotype. Ann Bot 95:177–190

    Article  PubMed  CAS  Google Scholar 

  • Laurie D, Bennett M (1985) Nuclear DNA content in the genera Zea and Sorghum—intergeneric, interspecific and intraspecific variation. Heredity 55:307–313

    Article  Google Scholar 

  • Lavergne S, Muenke NJ, Molofsky J (2010) Genome size reduction can trigger rapid phenotypic evolution in invasive plants. Ann Bot 105:109–116

    Article  PubMed  CAS  Google Scholar 

  • Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J (2010a) The sequence and de novo assembly of the giant panda genome. Nature 463:311–317

    Article  PubMed  CAS  Google Scholar 

  • Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, Grarup N, Guo Y, Hellman I, Jin X, Li Q, Liu J, Liu X, Sparso T, Tang M, Wu H, Wu R, Yu C, Zheng H, Astrup A, Bolund L, Holmkvist J, Jorgensen T, Kristiansen K, Schmitz O, Schwartz TW, Zhang X, Li R, Yang H, Wang J, Hansen T, Pedersen O, Nielsen R, Wang J (2010b) Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 42:969–972

    Article  PubMed  CAS  Google Scholar 

  • Li X, Zhu C, Lin Z, Wu Y, Zhang D, Bai G, Song W, Ma J, Muehlbauer GJ, Scanlon MJ, Zhang M, Yu J (2011) Chromosome size in diploid eukaryotic species centers on the average length with a conserved boundary. Mol Biol Evol 28:1901–1911

    Article  PubMed  CAS  Google Scholar 

  • Lippman Z, Gendrel A, Black M, Vaughn M, Dedhia N, McCombie W, Lavine K, Mittal V, May B, Kasschau K, Carrington J, Doerge R, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471–476

    Article  PubMed  CAS  Google Scholar 

  • Lisch D (2009) Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60:43–66

    Article  PubMed  CAS  Google Scholar 

  • Lister R, O’Malley R, Tonti-Filippini J, Gregory B, Berry C, Millar A, Ecker J (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536

    Article  PubMed  CAS  Google Scholar 

  • Lockton S, Gaut B (2010) The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata. BMC Evol Biol 10:10

    Article  PubMed  Google Scholar 

  • Ma J, Bennetzen J (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410

    Article  PubMed  CAS  Google Scholar 

  • Matzke M, Kanno T, Daxinger L, Huettel B, Matzke A (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21:367–376

    Article  PubMed  CAS  Google Scholar 

  • Meagher TR, Vassiliadis C (2005) Phenotypic impacts of repetitive DNA in flowering plants. New Phytol 168:71–80

    Article  PubMed  CAS  Google Scholar 

  • Meyers BC, Tingey SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11:1660–1676

    Article  PubMed  CAS  Google Scholar 

  • Ning ZM, Cox AJ, Mullikin JC (2001) SSAHA: a fast search method for large DNA databases. Genome Res 11:1725–1729

    Article  PubMed  CAS  Google Scholar 

  • Oliver MJ, Petrov D, Ackerly D, Falkowski P, Schofield OM (2007) The mode and tempo of genome size evolution in eukaryotes. Genome Res 17:594–601

    Article  PubMed  CAS  Google Scholar 

  • Peacock WJ, Dennis ES, Rhoades MM, Pryor AJ (1981) Highly repeated DNA-sequence limited to knob heterochromatin in maize. Proc Natl Acad Sci USA 78:4490–4494

    Article  PubMed  CAS  Google Scholar 

  • Petrov DA, Sangster TA, Johnston JS, Hartl DL, Shaw KL (2000) Evidence for DNA loss as a determinant of genome size. Science 287:1060–1062

    Article  PubMed  CAS  Google Scholar 

  • Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, Collura K, Brar D, Jackson S, Wing R, Panaud O (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262–1269

    Article  PubMed  CAS  Google Scholar 

  • Piperno DR, Ranere AJ, Holst I, Iriarte J, Dickau R (2009) Starch grain and phytolith evidence for early ninth millennium BP maize from the Central Balsas River Valley, Mexico. Proc Natl Acad Sci USA 106:5019–5024

    Article  PubMed  CAS  Google Scholar 

  • Poggio L, Rosato M, Chiavarino AM, Naranjo CA (1998) Genome size and environmental correlations in maize (Zea mays ssp. mays, Poaceae). Ann Bot 82:107–115

    Article  Google Scholar 

  • Ramakrishna W, Dubcovsky J, Park Y-J, Busso C, Emberton J, SanMiguel P, Bennetzen JL (2002) Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162:1389–1400

    PubMed  CAS  Google Scholar 

  • Rayburn AL, Auger JA (1990) Nuclear-DNA content variation in the ancient indigenous races of mexican maize. Acta Bot Neerlandica 39(2):197–202

    CAS  Google Scholar 

  • Rayburn A, Price H, Smith J, Gold J (1985) C-Band heterochromatin and DNA content in Zea mays. Am J Bot 72:1610–1617

    Article  Google Scholar 

  • Rayburn A, Biradar D, Bullock D, McMurphy L (1993) Nuclear DNA content in F1 hybrids of maize. Heredity 70:294–300

    Article  CAS  Google Scholar 

  • Ross-Ibarra J, Wright S, Foxe J, Kawabe A, DeRose-Wilson L, Gos G, Charlesworth D, Gaut B (2008) Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS One 3:e2411

    Article  PubMed  Google Scholar 

  • Ross-Ibarra J, Tenaillon M, Gaut B (2009) Historical divergence and gene flow in the genus zea. Genetics 181:1399–1413

    Article  PubMed  CAS  Google Scholar 

  • San Miguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Nat Genet 82:37–44

    CAS  Google Scholar 

  • Schmitz RJ, Schultz MD, Lewsey MG, O’Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science 334:369–373

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, Lanz C, Smith LM, Cao J, Fitz J, Warthmann N, Henz SR, Huson DH, Weigel D (2011) Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci USA 108:10249–10254

    Article  PubMed  CAS  Google Scholar 

  • Slotkin R, Freeling M, Lisch D (2005) Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat Genet 37:641–644

    Article  PubMed  CAS  Google Scholar 

  • Teixeira FK, Colot V (2009) Gene body DNA methylation in plants: a means to an end or an end to a means? EMBO J 28:997–998

    Article  PubMed  CAS  Google Scholar 

  • Tenaillon M, Hollister J, Gaut B (2010) A triptych of the evolution of plant transposable elements. Trends Plant Sci 15:471–478

    Article  PubMed  CAS  Google Scholar 

  • Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J (2011) Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biol Evol 3:219–229

    Article  PubMed  CAS  Google Scholar 

  • Tenaillon O, Rodriguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, Gaut BS (2012) The molecular diversity of adaptive convergence. Science 335:457–461

    Article  PubMed  CAS  Google Scholar 

  • Tito CM, Poggio L, Naranjo CA (1991) Cytogenetic studies in the genus Zea. 3. DNA content and heterochromatin in species and hybrids. Theor Appl Genet 83:58–64

    Article  Google Scholar 

  • Vitte C, Bennetzen J (2006) Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci USA 103:17638–17643

    Article  PubMed  CAS  Google Scholar 

  • Vitte C, Panaud O (2003) Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol Biol Evol 20:528–540

    Article  PubMed  CAS  Google Scholar 

  • Wang Q, Dooner H (2006) Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci USA 103:17644–17649

    Article  PubMed  CAS  Google Scholar 

  • Whitney KD, Baack EJ, Hamrick JL, Godt MJW, Barringer BC, Bennett MD, Eckert CG, Goodwillie C, Kalisz S, Leitch IJ, Ross-Ibarra J (2010) A role for nonadaptive processes in plant genome size evolution? Evolution 64:2097–2109

    PubMed  Google Scholar 

  • Wright SI, Le QH, Schoen DJ, Bureau TE (2001) Population dynamics of an Ac-like transposable element in self- and cross-pollinating arabidopsis. Genetics 158:1279–1288

    PubMed  CAS  Google Scholar 

  • Xu JJ, Zhao QA, Du PN, Xu CW, Wang BH, Feng Q, Liu QQ, Tang SZ, Gu MH, Han B, Liang GH (2010) Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics 11:656

    Article  PubMed  CAS  Google Scholar 

  • Zhang X (2008) The epigenetic landscape of plants. Science 320(5875):489–492

    Article  PubMed  CAS  Google Scholar 

  • Zilberman D, Henikoff S (2007) Genome-wide analysis of DNA methylation patterns. Development 134:3959–3965

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Ecology and Evolutionary Biology, UC Irvine, 321 Steinhaus Hall, Irvine, CA, 92617, USA

    Concepcion Muñoz-Diez & Brandon S. Gaut

  2. CNRS, UMR 0320 / UMR 8120 Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Ferme du Moulon, F-91190, Gif-sur-Yvette, France

    Clémentine Vitte & Maud I. Tenaillon

  3. The Department of Plant Sciences and The Genome Center and Center for Population Biology, UC Davis, 262 Robbins Hall, Davis, CA, 95616-5294, USA

    Jeffrey Ross-Ibarra

Authors
  1. Concepcion Muñoz-Diez
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Clémentine Vitte
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jeffrey Ross-Ibarra
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Brandon S. Gaut
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Maud I. Tenaillon
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Maud I. Tenaillon .

Editor information

Editors and Affiliations

  1. , Institut Jean-Pierre Bourgin (IJPB), INRA Versailles, UMR 1318, Versailles Cedex, 78026, France

    Marie-Angèle Grandbastien

  2. , Centre de Recerca en Agrigenomica (CRAG), CSIC-RTA-UAB, Barcelona, 08193, Spain

    Josep M. Casacuberta

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Muñoz-Diez, C., Vitte, C., Ross-Ibarra, J., Gaut, B.S., Tenaillon, M.I. (2012). Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content. In: Grandbastien, MA., Casacuberta, J. (eds) Plant Transposable Elements. Topics in Current Genetics, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31842-9_3

Download citation

Publish with us

Policies and ethics

Search

Navigation