Research
Evolutionary Biology of Genome Structure
Research in our lab addresses fundamental questions about genome structure and its role in plant evolution. Plant genomes are remarkably dynamic and structural change is tolerated in plants much more readily than in animals. One of the most frequent structural changes in plant genomes involves the duplication of the entire chromosome complement leading to a state known as polyploidy. Polyploids come in two general flavors: allopolyploids (hybrids of two different species) and autopolyploids (duplicated genomes of one species). See Figure 1 for details. Because polyploid genomes carry more loci of every gene than diploids do, it has been suggested that they are more adaptive to their environment and are superior to diploids in their ability to evolve.
Using the model genus Arabidopsis we study molecular mechanisms in polyploidy that could lead to speciation, adaptation, and genome evolution. Specifically, we have studied the role of epigenetics in transcriptional change, particularly with respect to conditionally mobile sequences in the genome called transposons. More recently we have used cytogenetics to address the question of genome stability in recent as compared to established polyploids.
A second related project aims to understand a peculiar process called floral reversion. Plants that undergo floral reversion abort the normally terminal developmental process of flowering. Instead of producing flowers and setting seed, reverting branches produce new inflorescences, and in some species new leaves, out of fully developed flowers. We have begun to analyze the molecular mechanisms for this phenomenon in polyploids of Arabidopsis suecica and are interested in finding out if genome duplication plays a role in this novel phenotype.
Polyploidy is an exciting field of study because it opens avenues of research into evolution, molecular biology, genetics, development, and ecological physiology.
All projects in the lab lend themselves well to independent research. If you are interested in joining the lab come and talk to me and I can suggest a number of specific projects to you. In the meantime you can read about our work in these selected publications. (Puget Sound students and alumni are noted with an asterisk.)
Publications
Pignatta, D, Dilkes, B, Yoo, SY, Henry, IM, Madlung, A, Doerge, RW, Chen, ZJ, Comai, L: Differential sensitivity of the Arabodopsis thaliana transcriptome and enhancers to the effects of genome doubling (2010) New Phytologist, 186, 194-206
McCullough, E*, Wright, KM*, Alvarez, A*, Clark, CP*, Rickoll, WL, Madlung, A.: Flower reversion in the natural allopolyploid Arabidopsis suecica (2010) New Phytologist, 186, 239-250
Madlung, A: Genome Organization and Gene Expression. Chapter 2 (2010) In: Plant Physiology, Taiz, L and Zeiger, E (eds.), Sinauer, 5th ed, 35-61
Bremer, M, Himelblau, E, Madlung, A: Introduction to the Statistical Analysis of Two-Color Microarray Data. (2010) In: Statistical Methods in Molecular Biology, Bang, H, Zhou, XK, Epps, HLV, Mazumdar, M (eds.), Humana Press, 285-311
Wright, KM*, Pires, JC, Madlung, A: Mitotic instability in resynthesized and natural polyploids of the genus Arabidopsis (Brassicaceae), (2009) American Journal of Botany, 96, 1656-1664
Wang, J., Tian, L., Lee, H. S., Wei, N.E., Jiang, H., Watson, B., Madlung, A., Osborn, T. C., Doerge, R. W., Comai, L., & Chen, Z. J. Genome-wide non-additive gene regulation in Arabidopsis allotetraploids. (2006) Genetics, 172, 507-517
Madlung, A, Tyagi, AP, Watson, B, Jiang, H, Kagochi, T*, Doerge, RW, Martienssen, R, Comai, L: Genomic changes in Arabidopsis polyploids (2005) The Plant Journal, 41, 221-230
Pontes, O, Neves, N, Silva, M, Lewis, MS, Madlung, A, Comai, L, Viegas W, Pikaard, CS: Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome (2004) Proceedings of the National Academy of Sciences (PNAS), 101, 52, 18240-18245
Madlung, A, and Comai, L: The effect of stress on genome regulation and structure. (2004) Annals of Botany, 94: 481-495
Wang, J Tian, L, Madlung, A, Lee, HS, Chen, M, Lee, JJ, Watson, B, Kagochi, T*, Comai, L, and Chen, ZJ: Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids (2004) Genetics, 167, 1961-1973
Comai, L, Madlung, A, Josefsson, C, Tyagi, A.: Do the different “heteromes” cause genomic shock in newly formed allopolyploids? (2003), Philosophical Transactions of the Royal Society of London, 358, 1149-1155
Osborn, TC, Pires, JC, Birchler, JA, Auger, D, Chen, ZJ, Lee, HS, Comai, L, Madlung, A Doerge, RW, Colot, V, Martienssen, RA: (2003) Understanding mechanisms of novel gene expression in polyploids (2003), Trends in Genetics, 19 (3), 141-147
Madlung, A., Masuelli, R., Watson, B., Reynolds, S., and Comai, L: Remodeling of DNA Methylation and Phenotypic and Transcriptional Changes in Synthetic Arabidopsis Allotetraploids. (2002) Plant Physiology, 129, 733-746
This page was last updated in September 2010.
