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Plant Genomes: From Sequence to Function Across Evolutionary Time

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Molecular Life Sciences
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Synopsis

It has only been a little over a decade since the first plant genome sequence was made available. Since then, major advancements in the understanding of not only plant genomes but also plant biology have been made. From genome sequence data, the overall distribution of genes, transposable elements, and other chromosome landmarks in multiple species that span the taxa within angiosperms and lower land plants is known. At the genome level, an area of active investigation is the structure and function of protein-coding genes, and their evolution as plant genomes undergoes rampant gene and genome duplication events. Indeed, access to genome sequence and annotation has revealed that all plant genomes contain a high number of paralogous gene families, which provide a template for diversification that can lead to phenotypic diversity. The application of the next-generation sequencing technology to plant genomes has enabled the sequencing of hundreds of genomes within a species. At a...

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References

  1. Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36:138–145

    Article  CAS  PubMed  Google Scholar 

  2. Gill BS, Appels R, Botha-Oberholster AM, Buell CR, Bennetzen JL, Chalhoub B, Chumley F, Dvorak J, Iwanaga M, Keller B, Li W, McCombie WR, Ogihara Y, Quetier F, Sasaki T (2004) A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics 168:1087–1096

    Article  PubMed Central  PubMed  Google Scholar 

  3. Haas BJ, Wortman JR, Ronning CM, Hannick LI, Smith RK Jr, Maiti R, Chan AP, Yu C, Farzad M, Wu D, White O, Town CD (2005) Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol 3:7

    Article  PubMed Central  PubMed  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  6. Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7:327

    Article  PubMed Central  PubMed  Google Scholar 

  7. Meyer IM (2007) A practical guide to the art of RNA gene prediction. Brief Bioinform 8:396–414

    Article  CAS  PubMed  Google Scholar 

  8. Brown JW, Waugh R (1989) Maize U2 snRNAs: gene sequence and expression. Nucleic Acids Res 17:8991–9001

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  10. He Y (2009) Control of the transition to flowering by chromatin modifications. Mol Plant 2:554–564

    Article  CAS  PubMed  Google Scholar 

  11. Lauria M, Rossi V (2011) Epigenetic control of gene regulation in plants. Biochim Biophys Acta 1809:369–378

    Article  CAS  PubMed  Google Scholar 

  12. Green BR (2011) Chloroplast genomes of photosynthetic eukaryotes. Plant J 66:34–44

    Article  CAS  PubMed  Google Scholar 

  13. Kubo T, Newton KJ (2008) Angiosperm mitochondrial genomes and mutations. Mitochondrion 8:5–14

    Article  CAS  PubMed  Google Scholar 

  14. Stupar RM, Lilly JW, Town CD, Cheng Z, Kaul S, Buell CR, Jiang J (2001) Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proc Natl Acad Sci U S A 98:5099–5103

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Bennett MD, Leitch IJ, Price HJ, Johnston JS (2003) Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb. Ann Bot 91:547–557

    Article  CAS  PubMed  Google Scholar 

  16. Somerville C, Koornneef M (2002) A fortunate choice: the history of Arabidopsis as a model plant. Nat Rev Genet 3:883–889

    Article  CAS  PubMed  Google Scholar 

  17. Adams MD, Soares MB, Kerlavage AR, Fields C, Venter JC (1993) Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nat Genet 4:373–380

    Article  CAS  PubMed  Google Scholar 

  18. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735–743

    Article  CAS  PubMed  Google Scholar 

  19. Weigel D, Mott R (2009) The 1001 genomes project for Arabidopsis thaliana. Genome Biol 10:107

    Article  PubMed Central  PubMed  Google Scholar 

  20. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC, Ecker JR (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653–657

    Article  PubMed  Google Scholar 

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

    Article  Google Scholar 

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Correspondence to Kevin L. Childs .

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© 2014 Springer Science+Business Media New York

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Childs, K.L., Buell, C.R. (2014). Plant Genomes: From Sequence to Function Across Evolutionary Time. In: Bell, E. (eds) Molecular Life Sciences. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6436-5_100-3

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  • DOI: https://doi.org/10.1007/978-1-4614-6436-5_100-3

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  • Online ISBN: 978-1-4614-6436-5

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