Plant genome structure and evolution, especially the nature of rearrangements and the contributions of transposable elements.
Molecular mapping using DNA probes, and now comprehensive DNA sequencing projects, have shown that gene content and order are significantly conserved between species, especially in closely related species. However, complex plant genomes like those in the angiosperms are relatively unstable, rearranging gene content and order at rates as much as 100-fold faster than mammalian genomes, for instance. We have begun to define the nature of these rearrangements and their mechanisms. Our preliminary data indicate that transposable elements are particularly clear sensors of these changes, many of which are caused by ectopic homologous recombination and illegitimate recombination. Ongoing and future studies will precisely determine the mechanisms of illegitimate recombination, will define the differences in the frequencies and types of these events in different plant lineages, and will measure how these processes contribute to the C value paradox. Bioinformatics and high throughput genomics are the key tools in these studies.
Recent related publications :
Bennetzen JL. (2007) Patterns in grass genome evolution. Curr Opin Plant Biol. 10(2):176-81. Pub Med Link
Ma J., Bennetzen J.L. (2006) Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. Proc Natl Acad Sci U S A. 103(2):383-8. Pub Med Link
Vitte C, Bennetzen JL. (2006) Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci USA 103(47):17638-4. Pub Med Link
Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KF, Messing J. (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Research. 16(10):1241-51. Pub Med Link
Emberton J, Ma J, Yuan Y, SanMiguel P, Bennetzen JL (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res. 15(10):1441-6. Pub Med link
Bennetzen, J.L., J. Ma and K. M. Devos (2005) Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 95(1):127-32. Pub Med link
Swigonova, Z., J. Lai, J. Ma, W. Ramakrishna, V. Llaca, J.L. Bennetzen, J. Messing (2004) Close split of sorghum and maize genome progenitors. Genome Res 14: 1916-1923. Pub Med link
Yuan, Y., P. J. SanMiguel and J.L. Bennetzen (2003) High Cot sequence analysis of the maize genome. Plant J ., 34:249-255. Pub Med link
Whitelaw,C.A.; Barbazuk,W.B.; Pertea,G.; Chan,A.P.; Cheung,F.; Lee,Y.; Zheng,L.; van Heeringen,S.; Karamycheva,S.; Bennetzen, J.L.; SanMiguel,P.; Lakey,N.; Bedell,J.; Yuan,Y.; Budiman,M.A.; Resnick,A.; Van Aken,S.; Utterback,T.; Riedmuller,S.; Williams,M.; Feldblyum,T.; Schubert,K.; Beachy,R.; Fraser,C.M.; Quackenbush,J. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120. Pub Med link
Bennetzen, J.L. (2002) The rice genome. Opening the door to comparative plant biology. Science 296:60-63. Pub Med link
Yuan, Y., P. J. SanMiguel and J. L. Bennetzen (2002) Methylation -spanning linker libraries link gene-rich regions and identify epigenetic boundaries in Zea mays . Genome Res . 12:1345-1349. Pub Med link