Abstract
Barley genome sequencing is lagging behind the status achieved for many other crop genomes although barley is ranking worldwide as fifth most important crop species. Whole genome sequencing of barley with classical Sanger sequencing technology was long meant to be too costly due to the very large genome size of more than 5 Gigabases. By the introduction of Next Generation Sequencing technology this situation has changed and fascinating new possibilities opened up for in depth barley genome analysis and whole genome sequencing. Genome composition has been revealed at unprecedented resolution. A linear gene order map comprising two thirds of all barley genes could be developed and the approach is currently adopted for other related and important cereal genomes like wheat and rye. Important technical limitations have been solved making even whole genome sequencing in barley a feasible endeavor. Provided these new possibilities, it is becoming obvious that soon sequencing per se is no longer the limiting factor but sequence assembly remains the challenge. This review will provide a brief summary of the recent developments in barley genome sequencing achieved since the introduction of Next Generation Sequencing.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Baird NA, Etter PD, Atwood TS et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376
Berkman P, Skarshewski A, Manoli S et al (2011a) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet. in press
Berkman PJ, Skarshewski A, Lorenc MT et al (2011b) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J 9:768–775
Chain PSG, Grafham DV, Fulton RS et al (2009) Genome project standards in a new era of sequencing. Science 326:236–237
Chevreux B, Wetter T, Suhei S (1999) Genome sequence assembly using signals and additional sequence information. Computer science and biology: proceedings of the German conference on bioinformatics (GCB), 99:45–56
Chutimanitsakun Y, Nipper R, Cuesta-Marcos A et al (2011) Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley. BMC Genomics 12:4
Doležel J, Kubaláková M, Paux E et al (2007) Chromosome-based genomics in the cereals. Chromosome Res 15:51–66
Elshire RJ, Glaubitz JC, Sun Q et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379
Eversole K, Graner A, Stein N (2009) Wheat and barley genome sequencing. In: Feuillet C, Muehlbauer GJ (eds) Genetics and genomics of the Triticeae. Springer pp 713–742
Feuillet C, Leach JE, Rogers J et al (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16:77–88
Flavell RB, Bennett MD, Smith JB, Smith DB (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12:257–269
Gnerre S, Maccallum I, Przybylski D et al (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108:1513–1518
Gore MA, Chia J-M, Elshire RJ et al (2009) A first-generation haplotype map of maize. Science 326:1115–1117
Hernandez P, Martis M, Dorado G et al (2011) Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J 69:377–386
Holt RA, Jones SJM (2008) The new paradigm of flow cell sequencing. Genome Res 18:839–846
Huang X, Feng Q, Qian Q et al (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800
Krattinger S, Wicker T, Keller B (2009) Map-based cloning of genes in Triticeae (wheat and barley). In: Feuillet C, Muehlbauer GJ (eds) Genetics and genomics of the Triticeae. Springer pp 337–357
Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412
Kurtz S, Narechania A, Stein J, Ware D (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9:517
Li R, Fan W, Tian G et al (2010) The sequence and de novo assembly of the giant panda genome. Nature 463:311–317
Manninen I, Schulman A (1993) BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol Biol 22:829–846
Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141
Mayer KFX, Taudien S, Martis M et al (2009) Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 151:496–505
Mayer KFX, Martis M, Hedley P et al (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–1263
Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46
Meyer M, Stenzel U, Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3:267–278
Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95:315–327
Myers EW, Sutton GG, Delcher AL et al (2000) A whole-genome assembly of Drosophila. Science 287:2196–2204
Paterson AH, Bowers JE, Bruggmann R et al (2009) The sorghum bicolor genome and the diversification of grasses. Nature 457:551–556
Phillippy A, Schatz M, Pop M (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 9:R55
Roach JC, Boysen C, Wang K, Hood L (1995) Pairwise end sequencing: a unified approach to genomic mapping and sequencing. Genomics 26:345–353
Rowe HC, Renaut S, Guggisberg A (2011) RAD in the realm of next-generation sequencing technologies. Mol Ecol 20:3499–3502
Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74:5463–5467
Sato K, Motoi Y, Yamaji N, Yoshida H (2011) 454 sequencing of pooled BAC clones on chromosome 3H of barley. BMC Genomics 12:246
Schulte D, Close TJ, Graner A et al (2009) The international barley sequencing consortium–at the threshold of efficient access to the barley genome. Plant Physiol 149:142–147
Service RF (2006) Gene sequencing: the race for the $1000 genome. Science 311:1544–1546
Simpson JT, Durbin R (2011) Efficient de novo assembly of large genomes using compressed data structures. Genome Res 22:549–556
Simpson J, Wong K, Jackman S et al (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117–1123
Sorokin A, Marthe F, Houben A et al (1994) Polymerase chain reaction mediated localization of RFLP clones to microisolated translocation chromosomes of barley. Genome 37:550–555
Staden R (1980) A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res 8:3673–3694
Stein N (2007) Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosome Res 15:21–31
Stein N, Graner A (2004) Map-based gene isolation in cereal genomes. In: Gupta P, Varshney R (eds) Cereal genomics. Kluwer Academic Publishers, Dordrecht, pp 331–360
Steuernagel B, Taudien S, Gundlach H et al (2009) De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics 10:547
Taudien S, Steuernagel B, Ariyadasa R et al (2011) Sequencing of BAC pools by different next generation sequencing platforms and strategies. BMC Res Notes 4:411
The International Barley Genome Sequencing Consortium (IBSC) (2012) A physical, genetical and functional sequence assembly of the barley genome. Nature 491:711–716
The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768
Vicient CM, Suoniemi A, Anamthawat-Jonsson K et al (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11:1769–1784
Vitulo N, Albiero A, Forcato C et al (2011) First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One 6:e26421
Wicker T, Schlagenhauf E, Graner A et al (2006) 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7:275
Wicker T, Narechania A, Sabot F et al (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
Wicker T, Taudien S, Houben A et al (2009) 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 J 59:712–722
Wicker T, Mayer KFX, Gundlach H et al (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23:1706–1718
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
Zhang H, Sreenivasulu N, Weschke W et al (2004) Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J 40:276–290
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Stein, N., Steuernagel, B. (2014). Advances in Sequencing the Barley Genome. In: Tuberosa, R., Graner, A., Frison, E. (eds) Genomics of Plant Genetic Resources. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7572-5_16
Download citation
DOI: https://doi.org/10.1007/978-94-007-7572-5_16
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-7571-8
Online ISBN: 978-94-007-7572-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)