The relationship between genome structure/evolution and gene function.
We are only beginning to understand how genome context (that is, the nature of the DNA/chromatin that surrounds genes) can influence gene function and gene evolution. The grasses that we study are particularly well-suited to such endeavors because genome structure changes so rapidly. We are using the full set of genomics tools, including bioinformatics, full genome sequencing, expression analyses and reverse genetics, to try to determine the relationship between genomic context and gene expression. In addition, we are using these same tools to answer one of the great questions in biology. Namely, what are the specific genetic changes that differentiate species? In order to pursue these studies from a strong foundation, we need to have full genome sequence information for many species of plants. Current approaches to genome sequencing are too expensive to permit analysis of more than a few species, so we have developed gene-enrichment technologies that will allow low cost and very quick sequencing of any complex genome (plant, animal, fungal or protist). These technologies are now being tested in a project to sequence and orient the gene space within the maize nuclear genome. TIGR Maize Genome
Recent related publications :
Liu R, Vitte C, Ma J, Mahama AA, Dhliwayo T, Lee M, Bennetzen JL. (2007) A GeneTrek analysis of the maize genome. Proc Natl Acad Sci U S A. 104: 11844-11849 Pub Med Link
Ma J, Wing RA, Bennetzen JL, Jackson SA. (2007) Plant centromere organization: a dynamic structure with conserved functions. Trends Genet. 23(3):134-9. Pub Med Link
Ma J, SanMiguel P, Lai J, Messing J, Bennetzen JL (2005) DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes. Genetics. 170(3):1209-20. Pub Med Link
Ma, Jianxin and J.L. Bennetzen (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 101:12404-12410. Pub Med link
Ilic , K., P. J. SanMiguel and J.L. Bennetzen (2003) A complex history of rearrangement in an orthologous region of the maize, sorghum and rice genomes. Proc. Natl. Acad. Sci . USA 100:12265-12270. Pub Med link