Skip to main content
SpringerLink
Log in

The Arabidopsis Genome and Its Use in Cereal Genomics

  • Chapter
Cereal Genomics

  • 835 Accesses

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 269.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 339.00
Price excludes VAT (USA)
  • Compact, lightweight 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Acarkan A., Rossberg M., Koch M., Schmidt R. Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella. Plant Jour 2000; 23:55–62

    CAS  Google Scholar 

  • Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., et al. The genome sequence of Drosophila melanogaster. Science 2000; 287:2185–2195

    Article  PubMed  Google Scholar 

  • Alonso J.M., Stepanova A.N., Leisse T.J., Kim C.J., Chen H., Shinn P., Stevenson D.K., Zimmerman J., Barajas P., Cheuk R., et al. Genome-Wide insertional mutagenesis of Arabidopsis thaliana. Science 2003; 301:653–657

    Article  PubMed  Google Scholar 

  • Anon. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 1998; 282:2012–2018

    Google Scholar 

  • Anon.. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium. The complete sequence of a heterochromatic island from a higher eukaryote. Cell 2000; 100:377–386

    Google Scholar 

  • Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. Jour Mol Biol 2001; 310:311–325

    CAS  Google Scholar 

  • Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet 2000; 25:25–29

    CAS  PubMed  Google Scholar 

  • Bennetzen J.L. Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 2002; 115:29–36

    Article  CAS  PubMed  Google Scholar 

  • Bennetzen J.L., Ramakrishna W. Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 2002; 48:821–827

    Article  CAS  PubMed  Google Scholar 

  • Blanchette M., Schwikowski B., Tompa M. An exact algorithm to identify motifs in orthologous sequences from multiple species. Proc Int Conf Intell Syst Mol Biol 2000; 8:37–45.

    CAS  PubMed  Google Scholar 

  • Blanchette M., Tompa M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res 2002; 12:739–748

    Article  CAS  PubMed  Google Scholar 

  • Boutet S., Vazquez F., Liu J., Beclin C., Fagard M., Gratias A., Morel J.B., Crete P., Chen X., Vaucheret H. Arabidopsis HEN1. A Genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr Biol 2003; 13:843–848

    Article  CAS  PubMed  Google Scholar 

  • Bowers J.E., Chapman B.A., Rong J., Paterson A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003; 422:433–438

    Article  CAS  PubMed  Google Scholar 

  • Brendel V., Kurtz S., Walbot V. Comparative genomics of Arabidopsis and maize: prospects and limitations. Genome Biol 2002; 3:REVIEWS1005

    Google Scholar 

  • Brett D., Pospisil H., Valcarcel J., Reich J., Bork P. Alternative splicing and genome complexity. Nature Genet 2002; 30:29–30

    Article  CAS  PubMed  Google Scholar 

  • Cardle L., Ramsay L., Milbourne D., Macaulay M., Marshall D., Waugh R. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 2000; 156:847–854

    CAS  PubMed  Google Scholar 

  • Chandler V.L., Brendel V. The Maize genome sequencing project. Plant Physiol 2002; 130:1594–1597

    Article  CAS  PubMed  Google Scholar 

  • Chory J., Ecker J.R., Briggs S., Caboche M., Coruzzi G.M., Cook D., Dangl J., Grant S., Guerinot M.L., Henikoff S., et al. National Science Foundation-sponsored workshop report: “The 2010 Project” functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiol 2000; 123:423–426

    Article  CAS  PubMed  Google Scholar 

  • Chothia C., Gough J., Vogel C., Teichmann S.A. Evolution of the Protein Repertoire. Science 2003; 300:1701–1703

    Article  CAS  PubMed  Google Scholar 

  • Feng Q., Zhang Y.J., Hao P., Wang S.Y., Fu G., Huang Y.C., Li Y., Zhu J.J., Liu Y.L., Hu X., et al. Sequence and analysis of rice chromosome 4. Nature 2002; 420:316–320

    Article  CAS  PubMed  Google Scholar 

  • Fransz P.F., Armstrong S., de Jong J.H., Parnell L.D., van Drunen G., Dean C., Zabel P., Bisseling T., Jones G.H. Integrated cytogenetic map of chromosome arm 4S of Athaliana: Structural organization of heterochromatic knob and centromere region. Cell 2000; 100:367–376

    Article  CAS  PubMed  Google Scholar 

  • Fulton T.M., Van der Hoeven R., Eannetta N.T., Tanksley S.D. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 2002; 14:1457–1467.

    Article  CAS  PubMed  Google Scholar 

  • Gale M.D., Devos K.M. Plant comparative genetics after 10 years. Science 1998; 282:656–659

    Article  CAS  PubMed  Google Scholar 

  • Goff S.A., Ricke D., Lan T.H., Presting G., Wang R.L., Dunn M., Glazebrook J., Sessions A., Oeller P., Varma H., et al. A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 2002; 296:92–100

    Article  CAS  PubMed  Google Scholar 

  • Guo H., Moose S.P. Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 2003; 15:1143

    CAS  PubMed  Google Scholar 

  • Gupta P.K., Rustgi S. Molecular markers from transcribed/expressed region of genome in higher plants. Funct Integr Genomics 2004 (in press)

    Google Scholar 

  • Haas B.J., Volfovsky N., Town C.D., Troukhan M., Alexandrov N., Feldmann K.A., Flavell R.B., White O., Salzberg S.L. Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol 2002; 3:RESEARCH0029

    Google Scholar 

  • Hillier L.D., Lennon G., Becker M., Bonaldo M.F., Chiapelli B., Chissoe S., Dietrich N., DuBuque T., Favello A., Gish W., et al. Generation and analysis of 280,000 human expressed sequence tags. Genome Res 1996; 6:807–828

    CAS  PubMed  Google Scholar 

  • Iseli C., Jongeneel C.V., Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1999:138–148

    Google Scholar 

  • Kasschau K.D., Xie Z., Allen E., Llave C., Chapman E.J., Krizan K.A., Carrington J.C. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev Cell 2003; 4:205–217

    Article  CAS  PubMed  Google Scholar 

  • Kidner C.A., Martienssen R.A. Macro effects of microRNAs in plants. Trends Genet 2003; 19:13–16

    Article  CAS  PubMed  Google Scholar 

  • Kikuchi S., Satoh K., Nagata T., Kawagashira N., Doi K., Kishimoto N., Yazaki J., Ishikawa M., Yamada H., Ooka H., et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 2003; 301:376–379

    Article  PubMed  Google Scholar 

  • Kota R., Rudd S., Facius A., Kolesov G., Thiel T., Zhang H., Stein N., Mayer K., Graner A. SniPping polymorphisms from the large barley EST collections. Mol Gen Genom 2003; 270: 24–33

    CAS  Google Scholar 

  • Ku H.M., Vision T., Liu J., Tanksley S.D. Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA 2000; 97:9121–9126

    Article  CAS  PubMed  Google Scholar 

  • Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al. Initial sequencing and analysis of the human genome. Nature 2001; 409:860–921

    Article  CAS  PubMed  Google Scholar 

  • Liang F., Holt I., Pertea G., Karamycheva S., Salzberg S.L., Quackenbush J. An optimized protocol for analysis of EST sequences. Nucl Acid Res 2000; 28:3657–3665

    CAS  Google Scholar 

  • Liu H., Sachidanandam R., Stein L. Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. Genome Res 2001; 11:2020–2026

    CAS  PubMed  Google Scholar 

  • Llave C., Xie Z., Kasschau K.D., Carrington J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002; 297:2053–2056

    Article  CAS  PubMed  Google Scholar 

  • Lukowitz W., Gillmor C.S., Scheible W.R. Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiol 2000; 123:795–806

    Article  CAS  PubMed  Google Scholar 

  • Mayer K., Murphy G., Tarchini R., Wambutt R., Volckaert G., Pohl T., Dusterhoft A., Stiekema W., Entian K.D., Terryn N., et al. Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana. Genome Res 2001; 11:1167–1174

    Article  CAS  PubMed  Google Scholar 

  • Mayer K., Schuller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Dusterhoft A., Stiekema W., Entian K.D., Terryn N., et al. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 1999; 402:769-+

    CAS  PubMed  Google Scholar 

  • McCombie W.R., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Yordan C., et al. The complete sequence of a heterochromatic island from a higher eukaryote. Cell 2000; 100:377–386

    CAS  Google Scholar 

  • Paterson A.H., Lan T.H., Reischmann K.P., Chang C., Lin Y.R., Liu S.C., Burow M.D., Kowalski S.P., Katsar C.S., DelMonte T.A., et al. Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nature Genet 1996; 14:380–382

    Article  CAS  PubMed  Google Scholar 

  • Pikaard C.S. Genomic change and gene silencing in polyploids. Trends Genet 2001; 17:675–677

    Article  CAS  PubMed  Google Scholar 

  • Pruitt R.E., Meyerowitz E.M. Characterization of the genome of Arabidopsis thaliana. Jour Mol Biol 1986; 187:169–183

    CAS  Google Scholar 

  • Rabinowicz P.D., Schutz K., Dedhia N., Yordan C., Parnell L.D., Stein L., McCombie W.R., Martienssen R.A. Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genet 1999; 23:305–308

    CAS  PubMed  Google Scholar 

  • Raizada M.N., Nan G.L., Walbot V. Somatic and germinal mobility of the RescueMu transposon in transgenic maize. Plant Cell 2001; 13:1587–1608

    Article  CAS  PubMed  Google Scholar 

  • Ramakrishna W., Emberton J., SanMiguel P., Ogden M., Llaca V., Messing J., Bennetzen J.L. Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex. Plant Physiol 2002; 130:1728–1738

    Article  CAS  PubMed  Google Scholar 

  • Ramalingam J., Vera Cruz C.M., Kukreja K., Chittoor J.M., Wu J.L., Lee S.W., Baraoidan M., George M.L., Cohen M.B., Hulbert S.H., et al. Candidate defense genes from rice, barley, and maize and their association with qualitative and quantitative resistance in rice. Mol Plant Microbe Interact 2003; 16:14–24

    CAS  PubMed  Google Scholar 

  • Redei G.P. A heurisic glance at the past of Arabidopsis genetics. In: C. Koncz, N.-H. Chua, J. Schell, Methods in Arabidopsis Research, World Scientific Publishing, Singapore, 1992, pp. 1–15

    Google Scholar 

  • Redei G.P., Koncz C. Classical mutagenesis, In: C. Koncz, N.-H. Chua, J. Schell, Methods in Arabidopsis Research, World Scientific Publishing, Singapore, 1992, pp. 16–82

    Google Scholar 

  • Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev 2002; 16:1616–1626

    Article  CAS  PubMed  Google Scholar 

  • Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., Bartel D.P. Prediction of plant microRNA targets. Cell 2002; 110:513–520

    Article  CAS  PubMed  Google Scholar 

  • Rossberg M., Theres K., Acarkan A., Herrero R., Schmitt T., Schumacher K., Schmitz G., Schmidt R. Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. Plant Cell 2001; 13:979–988

    Article  CAS  PubMed  Google Scholar 

  • Rudd S. Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 2003, 8:7:321–329

    Article  CAS  PubMed  Google Scholar 

  • Rudd S., Mewes H.W., Mayer K.F. Sputnik: a database platform for comparative plant genomics. Nucl Acids Res 2003; 31:128–132

    Article  CAS  PubMed  Google Scholar 

  • Salse J., Piegu B., Cooke R., Delseny M. Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice sequencing project. Nucleic Acids Res 2002; 30:2316–2328

    Article  CAS  PubMed  Google Scholar 

  • Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y., Wu J.Z., Niimura Y., Cheng Z.K., Nagamura Y., et al. The genome sequence and structure of rice chromosome 1. Nature 2002; 420:312–316

    Article  CAS  PubMed  Google Scholar 

  • Schmid K.J., Sorensen T.R., Stracke R., Torjek O., Altmann T., Mitchell-Olds T., Weisshaar B. Large-Scale Identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res 2003; 13:1250–1257

    Article  PubMed  Google Scholar 

  • Schmidt R. Synteny: recent advances and future prospects. Curr Opin Plant Biol 2000; 3:97–102

    Article  CAS  PubMed  Google Scholar 

  • Schoof H. Towards interoperability in genome databases: The MatDB (MIPS Arabidopsis thaliana Database) experience. Comp Funct Genom 2003; 4: 255–258

    Article  CAS  Google Scholar 

  • Schoof H., Karlowski W.M. Comparison of rice and Arabidopsis annotation. Curr Opin Plant Biol. 2003; 6:106–12

    Article  CAS  PubMed  Google Scholar 

  • Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science 2002; 296:141–145

    Article  PubMed  Google Scholar 

  • Stein L.D. Integrating biological databases. Nature Rev Genet 2003; 4:337–345

    CAS  Google Scholar 

  • TAGI. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000; 408:796–815

    Google Scholar 

  • The Rice Chromosome 10 Consortium In-depth view of structure, activity, and evolution of rice chromosome 10. Science 2003; 300:1566–1569

    Google Scholar 

  • Tompa M. Identifying functional elements by comparative DNA sequence analysis. Genome Res 2001; 11:1143–1144

    Article  CAS  PubMed  Google Scholar 

  • Vandepoele K., Saeys Y., Simillion C., Raes J., Van De P.Y. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res 2002; 12:1792–1801

    Article  CAS  PubMed  Google Scholar 

  • van Dodeweerd A.M., Hall C.R., Bent E.G., Johnson S.J., Bevan M.W., Bancroft I. Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana. Genome 2001; 42:887–892

    Google Scholar 

  • Varshney R.K., Thiel T., Stein N., Langridge P., Graner A. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 2002; 7:537–546

    CAS  PubMed  Google Scholar 

  • Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., et al. The sequence of the human genome. Science 2001; 291:1304-+

    Article  CAS  PubMed  Google Scholar 

  • Ware D., Jaiswal P., Ni J., Pan X., Chang K., Clark K., Teytelman L., Schmidt S., Zhao W., Cartinhour S., et al. Gramene: a resource for comparative grass genomics. Nucleic Acids Res 2002; 30:103–105

    Article  CAS  PubMed  Google Scholar 

  • Wray G.A, Hahn M.W., Abouheif E., Balhoff J.P., Pizer M., Rockman M.V., Romeno L.A. The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 2003; 20: 1377–1419.

    CAS  PubMed  Google Scholar 

  • Wasserman W.W., Palumbo M., Thompson W., Fickett J.W., Lawrence C.E. Human-mouse genome comparisons to locate regulatory sites. Nature Genet 2000; 42:225–228

    Google Scholar 

  • Wendel J.F. Genome evolution in polyploids. Plant Mol Biol 2000; 42:225–249

    Article  CAS  PubMed  Google Scholar 

  • Wong G.K.S., Wang J., Tao L., Tan J., Zhang J.G., Passey D.A., Yu J. Compositional gradients in Gramineae genes. Genome Res 2002; 12:851–856

    Article  CAS  PubMed  Google Scholar 

  • Yano M., Katayose Y., Ashikari M., Yamanouchi U., Monna L., Fuse T., Baba T., Yamamoto K., Umehara Y, Nagamura Y., et al. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 2000; 12:2473–2483

    Article  CAS  PubMed  Google Scholar 

  • Yu J., Hu S.N., Wang J., Wong G.K.S., Li S.G., Liu B., Deng Y.J., Dai L., Zhou Y., Zhang X.Q., et al. A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 2002; 296:79–92

    CAS  PubMed  Google Scholar 

  • Yuan Y., SanMiguel P.J., Bennetzen J.L. High-Cot sequence analysis of the maize genome. Plant Jour 2003; 34:249–255

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. National Research Centre for Environment and Health (GSF), MIPS, Institute for Bioinformatics, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany

    Klaus Mayer, Stephen Rudd & Heiko Schoof

Authors
  1. Klaus Mayer
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stephen Rudd
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Heiko Schoof
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Klaus Mayer .

Editor information

Editors and Affiliations

  1. Ch Charan Singh University, Meerut, India

    P. K. Gupta

  2. Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

    R. K. Varshney

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Kluwer Academic Publishers

About this chapter

Cite this chapter

Mayer, K., Rudd, S., Schoof, H. (2004). The Arabidopsis Genome and Its Use in Cereal Genomics. In: Gupta, P.K., Varshney, R.K. (eds) Cereal Genomics. Springer, Dordrecht. https://doi.org/10.1007/1-4020-2359-6_17

Download citation

Publish with us

Policies and ethics

Search

Navigation