Chapter 2 References

Textbook

Nuclear Genome Organization

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Kato, A., Lamb, J. C., and Birchler, J. A. (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc. Natl. Acad. Sci. USA 101: 13554–13559.

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Leitch, A. R., and Leitch, I. J. (2008) Genomic plasticity and the diversity of polyploid plants. Science 320: 481–483.

Leitch, A. R, and Leitch, I. J. (2012) Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytol. 194: 629–646.

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Ma, J., Wing, R. A., Bennetzen, J. L., and Jackson, S. A. (2007) Plant centromere organization: a dynamic structure with conserved functions. Trends Genet. 23: 134–139.

Madlung, A., and Wendel, J. F. (2013) Genetic and epigenetic aspects of polyploid evolution in plants. Cytogenet. Genome Res. 140: 270–285.

Madlung, A., Masuelli, R., Watson, B., Reynolds, S., and Comai, L. (2002) Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol. 129: 733–746.

Madlung, A., Tyagi, A. P., Watson, B., Jiang, H., Kagochi, T., Doerge, R. W., Martienssen, R., and Comai, L. (2005) Genomic changes in Arabidopsis polyploids. Plant J. 41: 221–230.

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Osborn, T. C., Pires, J. C., Birchler, J. A., Auger, D., Chen, Z. J., Lee, H. S., Comai, L., Madlung, A. Doerge, R. W., Colot, V., et al. (2003) Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19: 141–147.

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Parisod, C., Alix, K., Just, J., Petit, M., Sarilar, V., Mhiri, C., Ainouche, M., Chalhoub, B., and Grandbastien, M.-A. (2010) Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol. 186: 37–45.

Pecinka, A., Fang, W., Rehmsmeier, M., Levy, A., and Mittelsten Scheid, O. (2011) Polyploidization increases meiotic recombination frequency in Arabidopsis. BMC Biol. 9: 24.

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Pires, J. C., Lim, K. Y., Kovarik, A., Matyasek, R., Boyd, A., Leitch, A. R., Leitch, I. J., Bennett, M. D., Soltis, P. S., and Soltis, D. E. (2004) Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors. Am. J. Bot. 91: 1022–1035.

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Riddle, N. C., and Birchler, J. A. (2008) Comparative analysis of inbred and hybrid maize at the diploid and tetraploid levels. Theor. Appl. Genet. 116: 563–576.

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Schnable, J. C., Springer, N. M., and Freeling, M. (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. USA 108: 4069–4074.

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Tang, H., and Lyons, E. (2012) Unleashing the genome of Brassica rapa. Front. Plant Sci. [DOI: 10.3389/fpls.2012.00172]

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Tiang, C. L., He, Y., and Pawlowski, W. P. (2012) Chromosome organization and dynamics during interphase, mitosis, and meiosis in plants. Plant Physiol. 158: 26–34.

Wang, J., Tian, L., Lee, H. S., Wei, N. E., Jiang, H., Watson, B., Madlung, A., Osborn, T. C., Doerge, R. W., Comai, L., et al. (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172: 507–517.

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Yoo, M. J., Szadkowski, E., and Wendel, J. F. (2013) Homoeolog expression bias and expression level dominance in allopolyploid cotton. Heredity 110: 171–180.

Zhou, R., Moshgabadi, N., and Adams, K. L. (2011) Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids. Proc. Natl. Acad. Sci. USA 108: 16122–16127.

Plant Cytoplasmic Genomes: Mitochondria and Plastids

Allen, J. F. (2003) The function of genomes in bioenergetic organelles. Phil. Trans. R. Soc. Lond., B., Biol. Sci. 358: 19–37.

Bendich, A. (2013) DNA abandonment and the mechanisms of uniparental inheritance of mitochondria and chloroplasts. Chromosome Res. 21: 287–296.

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Transcriptional Regulation of Nuclear Gene Expression

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Posttranscriptional Regulation of Nuclear Gene Expression

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Tools for Studying Gene Function

Citovsky, V., Kozlovsky, S. V., Lacroix, B., Zaltsman, A., Dafny-Yelin, M., Vyas, S., Tovkach, A., and Tzfira, T. (2007) Biological systems of the host cell involved in Agrobacterium infection. Cell. Microbiol. 9: 9–20.

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Genetic Modification of Crop Plants

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Web Topics

Guo, F., Hu, S.-H., Yuan, Z., Zee, S.-Y., and Han, Y. (2005) Paternal cytoplasmic transmission in Chinese pine (Pinis tabuleaformis). Protoplasma 225: 5–14

Mogensen, L. (1996) The hows and whys of cytoplasmic inheritance in seed plants. Am. J. Bot. 83: 383–404.

Oldenburg, D. J., and Bendich, A. J. (1998) The structure of mitochondrial DNA from the liverwort, Marchantia polymorpha. J. Mol. Biol. 276: 745–758.

Oldenburg, D. J., and Bendich, A. J. (2004) Most chloroplast DNA of maize seedlings in linear molecules with defined ends and branched forms. J. Mol. Biol. 335: 953–970

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