Textbook

Nuclear Genome Organization

Adams, K. L., Cronn, R., Percifield, R., and Wendel, J. F. (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA 100: 4649­–4654.

Birchler, J. A., Gao, Z., Sharma, A., Presting, G. G., and Han, F. (2011) Epigenetic aspects of centromere function in plants. Curr. Opin. Plant Biol. 14: 217­–222.

Bomblies, K., and Madlung, A. (2014) Polyploidy in the Arabidopsis genus. Chromosome Res. 22: 117–134.

Chao, D. Y., Dilkes, B., Luo, H., Douglas, A., Yakubova, E., Lahner, B., and Salt, D. E. (2013) Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science 341: 658–659.

Chen, Z. J. (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu. Rev. Plant Biol. Mol. Biol. 58: 377–406.

Chester, M., Gallagher, J. P., Symonds, V. V., Cruz da Silva, A. V., Mavrodiev, E. V., Leitch, A. R., Soltis, P. S., and Soltis, D. E. (2012) Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc. Natl. Acad. Sci. USA 109: 1176–1181.

Comai, L. (2005) The advantages and disadvantages of being polyploid. Nat. Rev. Genet. 6: 836–846.

Eickbush, T. H., and Malik, H. S. (2002) Origins and evolution of retrotransposons. In Mobile DNA II, N. L. Craig, R. Craigie, M. Gellert, and A. M. Lambowitz, eds., ASM Press, Washington, DC., pp. 1111–1144.

Feldman, M., Liu, B., Segal, G., Abbo, S., Levy, A. A., and Vega, J. M. (1997) Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homologous chromosomes. Genetics 147: 1381–1387.

Gill, N., Hans, C. S., and Jackson, S. (2008) An overview of plant chromosome structure. Cytogenet. Genome Res. 120: 194–201.

Grandont, L., Jenczewski, E., and Lloyd, A. (2013) Meiosis and its deviations in polyploid plants. Cytogenet Genome Res. 140: 171–184.

Hegarty, M. J., Batstone, T., Barker, G. L., Edwards, K. J., Abbott, R. J., and Hiscock, S. J. (2011) Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae). Mol. Ecol. 20: 105–113.

Heslop-Harrison, J. S. (2012) Genome evolution: extinction, continuation or explosion? Curr. Opin. Plant Biol. 15: 115–121.

Heslop-Harrison, J. S., and Schmidt, T. (2007) Plant nuclear genome composition. In Encyclopedia of Life Sciences, John Wiley & Sons, Ltd., Chichester, UK, http://www.els.net/ [DOI: 10.1002/9780470015902.a0002014.pub2].

Ibarra-Laclette, E., Lyons, E., Hernandez-Guzman, G., Perez-Torres, C. A., Carretero-Paulet, L., Chang, T.-H., Lan, T., Welch, A. J., Juarez, M. J. A., Simpson, J., et al. (2013) Architecture and evolution of a minute plant genome. Nature 498: 94–98.

Jiang, J., Birchler, J., Parrott, W. A., and Dawe, R. K. (2003) A molecular view of plant centromeres. Trends Plant Sci. 8: 570–575.

Jiao, Y., Wickett, N. J, Ayyampalayam, S., Chanderbali, A. S., Landherr, L., Ralph, P. E., Tomsho, L. P., Hu, Y., Liang, H., Soltis, P. S., et al. (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97–100.

Kashkush, K., Feldman, M., and Levy, A. A. (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 33: 102–106.

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.

Kato, A., Vega, J. M., Han, F., Lamb, J. C., and Birchler, J. A. (2005) Advances in plant chromosome identification and cytogenetic techniques. Curr. Opin. Plant Biol. 8: 148–154.

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.

Lynch, M., and Force, A. (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459–473.

Ma, H. (2005) Molecular genetic analyses of microsporogenesis and microgametogenesis in flowering plants. Annu. Rev. Plant Biol. 56: 393–434.

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.

Mayrose, I., Zhan, S. H., Rothfels, C. J., Magnuson-Ford, K., Barker, M. S., Rieseberg, L. H., and Otto, S. P. (2011). Recently formed polyploid plants diversify at lower rates. Science 333: 1257.

Miura, A., Yonebayashi, S., Watanabe, K., Toyama, T., Shimadak, H., and Kakutani, T. (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411: 212–214.

Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A., Lin, Y. C., Scofield, D. G., Vezzi, F., Delhomme, N., Giacomello, S., Alexeyenko, A., et al. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497: 579–584.

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.

Parisod, C., Salmon, A., Zerjal, T., Tenaillon, M., Grandbastien, M. A., and Ainouche, M. (2009) Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol. 184: 1003–1015.

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.

Pellicer, J., Fay, M. F., and Leitch, I. J. (2010) The largest eukaryotic genome of them all? Bot. J. Linn. Soc. 164: 10–15.

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.

Ramsey, J., and Schemske, D. (1998) Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu. Rev. Ecol. Syst. 29: 467–501.

Rapp, R., Udall, J., and Wendel, J. (2009) Genomic expression dominance in allopolyploids. BMC Biol. 7: 18.

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.

Riddle, N. C., Kato, A., and Birchler, J. A. (2006) Genetic variation for the response to ploidy change in Zea mays L. Theor. Appl. Genet.114: 101–111.

Salmon, A., Ainouche, M. L., and Wendel, J. F. (2005) Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol. Ecol. 14: 1163–1175.

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.

"TAIR10." Arabidopsis.org. (2010) ftp://ftp.Arabidopsis.org/home/tair/Genes/TAIR10_genome_release/README_TAIR10.txt.

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

Tate, J., Joshi, P., Soltis, K., Soltis, P., and Soltis, D. (2009) On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae). BMC Plant Biol. 9: 80.

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.

Wolfe, K. H. (2001) Yesterday’s polyploidization and the mystery of diploidization. Nat. Rev. Genet. 2: 333–341.

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.

Sloan, D. B., Alverson, A. J., Chuckalovcak, J. P., Wu, M., McCauley, D. E., Palmer, J. D., and Taylor, D. R. (2012) Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol. 10: e1001241. [DOI: 10.1371/journal.pbio.1001241].

Transcriptional Regulation of Nuclear Gene Expression

Blake, M. C., Jambou, R. C., Swick, A. G., Kahn, J. W., and Azizkhan, J. C. (1990) Transcriptional initiation is controlled by upstream GC-box interactions in a TATAA-less promoter. Mol. Cell Biol. 10: 6632–6641.

Lin, H., Huang, L. F. Su, H.-C., and Jeng, S.-T. (2009) Effects of the multiple polyadenylation signal AAUAAA on mRNA 30-end formation and gene expression. Planta 230: 699–712.

Liu, C., Lu, F., Cui, X., and Cao, X. (2010) Histone methylation in higher plants. Annu. Rev. Plant Biol. 61: 395–420.

Loke, J. C., Stahlberg, E. A., Strenski, D. G., Haas, B. J., Wood, P. C., and Li, Q. Q. (2005) Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol. 138: 1457–1468.

Maston, G. A., Evans, S. K., and Green, M. R. (2006) Transcriptional regulatory elements in the human genome. Annu. Rev. Genomics Hum. Genet. 7: 29–59.

Mantovani, R. (1999) The molecular biology of the CCAAT-binding factor NF-Y. Gene 239: 15–27

Smale, S. T., and Kadonaga, J. T. (2003) The RNA polymerase II core promoter. Annu. Rev. Biochem. 72: 449–479.

Yang, C., Bolotin, E., Jiang, T., Sladek, F. M., and Martinez, E. (2007) Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 389: 52–65.

Posttranscriptional Regulation of Nuclear Gene Expression

Castel, S., and Martienssen, R. A. (2013) RNA interference in the nucleus: Roles for small RNAs in transcription, epigenetics and beyond. Nat. Rev. Genet. 14: 100–112.

Chapman, E., and Carrington, J. C. (2007) Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 8: 884–896.

Chen, X. (2009) Small RNAs and their roles in plant development. Annu. Rev. Cell Dev. Biol. 25: 21–44.

Coux, O., Tanaka, K., and Goldberg, A. L. (1996) Structure and functions of the 20S and 26S proteasomes. Annu. Rev. Biochem. 65: 2069–2076.

Czech, B., and Hannon, G. J. (2011) Small RNA sorting: matchmaking for argonautes. Nat. Rev. Gen. 12: 19–31.

Ghildiyal, M., and Zamore, P. D. (2009). Small silencing RNAs: an expanding universe. Nat. Rev. Gen. 10: 94–108.

Green, P. J. (1993) Control of mRNA stability in higher plants. Plant Physiol. 102: 1065–1070.

Hollams, E. M., Giles, K. M., Thomson, A. M., and Leedman, P. J. (2002) mRNA stability and the control of gene expression: implications for human disease. Neurochem. Res. 27: 957–980.

Lam, E. (1997) Nucleic acids and proteins. In Plant Biochemistry, P. M. Dey and J. B. Harborne, eds., Academic Press, San Diego, CA, pp. 316–352.

Mlotshwa, S., Pruss, G. J., and Vance, V. (2008) Small RNAs in viral infection and host defense. Trends Plant Sci. 13: 375–382.

Napoli, C., Lemieux. C., and Jorgensen, R. (1990) Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2: 279–289.

Parker, R. (2012) RNA degradation in Saccharomyces cerevisae. Genetics 191: 671–702.

Ramachandran, V., and Chen, X. (2008) Small RNA metabolism in Arabidopsis. Trends Plant Sci. 13: 368–374.

Song, J.-J., Smith, S. K., Hannon, G. J., and Joshua-Tor, L. (2004) Crystal structure of argonaute and its implications for RISC slicer activity. Science 305: 1434­–1437.

Wang, M. B., Masuta, C., Smith, N. A., and Shimura, H. (2012) RNA silencing and plant viral diseases. Mol Plant Microbe Interact. 25: 1275–1285.

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.

Dafny-Yelin, M., Levy, A., and Tzfira, T. (2008) The ongoing saga of Agrobacterium–host interactions. Trends Plant Sci. 13: 102–105.

Foss, E. J., Radulovic, D., Shaffer, S. A., Ruderfer, D. M., Bedalov, A., Goodlet, D. R., and Kruglyak, L. (2007) Genetic basis of proteome variation in yeast. Nat Genet. 39: 1369–1375.

Garber, M., Grabherr, M. G., Guttman, M., and Trapnell, C. (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods 8: 469–477.

Genetic Modification of Crop Plants

Golden Rice Humanitarian Board: www.goldenrice.org, accessed May 31st, 2013.

Paine, J. A., Shipton, C. A., Chaggar, S., Howells, R. M., Kennedy, M. J., Vernon, G., Wright, S. Y., Hinchliffe, E., Adams, J. L., Silverstone, A. L., et al. (2005) Improving the nutritional value of golden rice through increased pro-vitamin A content. Nat Biotech. 23: 482–487.

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World Health Organization: http://www.who.int/foodsafety/publications/biotech/20questions/en/. Accessed May 31st 2013.

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