A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley

Plant Journal

Volumn 59, Issue 5, 2009, Pages 712-722

  Wicker, Thomas ^a   Taudien, Stefan ^b   Houben, Andreas ^c   Keller, Beat ^a   Graner, Andreas ^c   Platzer, Matthias ^b   Stein, Nils ^c  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b FRITZ LIPMANN INSTITUTE   (Germany)

^c LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

454 whole genome snapshot; Conserved non coding sequence; Fluorescence in situ hybridization; Gene content; Genome size evolution; Repetitive DNA

Indexed keywords

PLANT DNA;

ARTICLE; BARLEY; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; PLANT GENOME; TRANSPOSON; WHEAT;

DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; EVOLUTION, MOLECULAR; GENOME, PLANT; HORDEUM; SEQUENCE ANALYSIS, DNA; TRITICUM;

HORDEUM; TRITICUM AESTIVUM;

EID: 69249142634     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2009.03911.x     Document Type: Article

References (40)

1. Bennett, M.D. Smith, J.B. (1976) Nuclear DNA amounts in angiosperms. Philos. Trans. R. Soc. Lond. B Biol. Sci. 274, 227 274.
2. Bossolini, E., Wicker, T., Knobel, P.A. Keller, B. (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice, implications for wheat genomics and grass genome annotation. Plant J. 49, 704 717.
3. Bruggmann, R., Bharti, A.K., Gundlach, H. et al. (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16, 1241 1251.
4. Bureau, T.E. Wessler, S.R. (1994) Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc. Natl Acad. Sci. USA, 91, 1411 1415.
5. Chalupska, D., Lee, H.Y., Faris, J.D., Evrard, A., Chalhoub, B., Haselkorn, R. Gornicki, P. (2008) Acc homoeoloci and the evolution of wheat genomes. Proc. Natl Acad. Sci. USA, 105, 9691 9696.
6. Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A.J., Müller, W.E., Wetter, T. Suhai, S. (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 1147 1159.
7. Devos, K.M., Brown, J.K.M. Bennetzen, J.L. (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12, 1075 1079.
8. Devos, K.M., Ma, J., Pontaroli, A.C., Pratt, L.H. Bennetzen, J.L. (2005) Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proc. Natl Acad. Sci. USA, 102, 19243 19248.
9. Houben, A., Orford, S.J. Timmis, J.N. (2006) In situ hybridization to plant tissues and chromosomes. Methods Mol. Biol. 326, 203 218.
10. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793 800.
11. Kalendar, R., Tanskanen, J., Immonen, S., Nevo, E. Schulman, A.H. (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl Acad. Sci. USA, 97, 6603 6607.
12. Leister, D. (2005) Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet. 21, 655 663.
13. Macas, J., Neumann, P. Navratilova, A. (2007) Repetitive DNA in the pea (Pisum sativum L.) genome, comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics, 8, 427.
14. Mardis, E.R. (2008) The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133 141.
15. Margulies, M., Egholm, M., Altman, W.E. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376 380.
16. Messing, J., Bharti, A.K., Karlowski, W.M. et al. (2004) Sequence composition and genome organization of maize. Proc. Natl Acad. Sci. USA 101, 14349 14354.
17. Meyers, B.C., Tingey, S.V. Morgante, M. (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res., 11, 1660 1676.
18. Paterson, A.H., Bowers, J.E., Chapman, B.A., Peterson, D.G., Rong, J. Wicker, T. (2004) Comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity. Curr. Opin. Biotechnol. 15, 120 125.
19. Paterson, A.H., Bowers, J.E., Bruggmann, R. et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457, 551 556.
20. Pereira, V. (2004) Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol. 5, R79.
21. Piegu, B., Guyot, R., Picault, N. et al. (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions. Genome Res. 16, 1262 1269.
22. Pourkheirandish, M., Wicker, T., Stein, N., Fujimura, T. Komatsuda, T. (2007) Analysis of the barley chromosome 2 region containing the six-rowed spike gene Vrs1 reveals a breakdown of rice-barley micro collinearity by a transposition. Theor. Appl. Genet. 114, 1357 1365.
23. Qi, L.L., Echalier, B., Chao, S. et al. (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics, 168, 701 712.
24. Sabot, F., Guyot, R., Wicker, T., Chantret, N., Laubin, B., Chalhoub, B., Leroy, P., Sourdille, P. Bernard, M. (2005) Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol. Genet. Genomics, 274, 119 130.
25. SanMiguel, P. Bennetzen, J.L. (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 82, S37 S44.
26. SanMiguel, P.J., Ramakrishna, W., Bennetzen, J.L., Busso, C.S. Dubcovsky, J. (2002) Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A(m). Funct. Integr. Genomics, 2, 70 80.
27. Shendure, J. Ji, H. (2008) Next-generation DNA sequencing. Nat Biotechnol. 26, 1135 1145.
28. Shirasu, K., Schulman, A.H., Lahaye, T. Schulze-Lefert, P. (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10, 908 915.
29. Soleimani, V.D., Baum, B.R. Johnson, D.A. (2006) Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome. Genome, 49, 389 396.
30. Swaminathan, K., Varala, K. Hudson, M.E. (2007) Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. BMC Genomics, 8, 132.
31. Swigonová, Z., Bennetzen, J.L. Messing, J. (2005) Structure and evolution of the r/b chromosomal regions in rice, maize and sorghum. Genetics, 169, 891 906. (Pubitemid 40404320)
32. Takahashi, C., Marshall, J.A., Bennett, M.D. Leitch, I.J. (1999) Genomic relationships between maize and its wild relatives. Genome, 42, 1201 1207.
33. Vicient, C.M., Kalendar, R., Anamthawat-Jonsson, K. Schulman, A.H. (1999) Structure, functionality, and evolution of the BARE-1 retrotransposon of barley. Genetica, 107, 53 63.
34. Vitte, C. Panaud, O. (2005) LTR retrotransposons and flowering plant genome size, emergence of the increase/decrease model. Cytogenet. Genome Res. 110, 91 107.
35. Vitte, C., Panaud, O. Quesneville, H. (2007) LTR retrotransposons in rice (Oryza sativa L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics, 8, 218.
36. Wicker, T. Keller, B. (2007) Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res. 17, 1072 1081.
37. Wicker, T., Yahiaoui, N., Guyot, R., Schlagenhauf, E., Liu, Z.D., Dubcovsky, J. Keller, B. (2003) Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat. Plant Cell, 15, 1186 1197.
38. Wicker, T., Schlagenhauf, E., Graner, A., Close, T.J., Keller, B. Stein, N. (2006) 454 sequencing put to the test using the complex genome of barley. BMC Genomics, 7, 275.
39. Wicker, T., Sabot, F., Hua-Van, A. et al. (2007a) A unified classification system for eukaryotic transposable elements. Nat Rev. Genet. 8, 973 982.
40. Wicker, T., Narechania, A., Sabot, F., Stein, J., Giang, V.T.H., Graner, A., Ware, D. Stein, N. (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9, 518.