Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Fractionation And Intragenomic Footprinting In Plants

Michael Freeling¹ , Eric Lyons ¹ , Brent Pedersen² , Lakshmi Rapaka¹ , Brian C. Thomas²

¹  Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720

²  College of Natural Resources, University of California, Berkeley, CA 94720

Our novel blast Viewer aligns any region of Arabidopsis with any other (http://synteny.cnr.berkeley.edu/AtCNS/). Using this Viewer, we proofed the A. Paterson group’s alpha pairs (2003), included our additional pairs, making a total of 3197 pairs, and then analyzed the sequence patterns of fractionation and conservation for coding and noncoding DNA. Alpha pairs are remnants from a fractionated tetraploid. Conclusions. 1) Fractionation from the tetraploid was biased to one or the other of the original parental chromosomes, implying an epigenetic marking step. 2) Fractionation left clusters of retained genes. These clusters are rich in regulatory genes and genes encoding proteins that interact, predicted by the gene balance hypothesis (see Birchler et al., 2005. Trends Genet. 21: 219); fractionation might duplicate functional modules. 3) We found 14,941 alphaCNSs (conserved noncoding sequences). Data fit with previous maize-rice data: upstream transcription factors and some other genes are rich in CNSs. 4) Intragenomic footprinting uncovered thousands of annotation errors from small to large, and some missed genes. 5) The function of CNSs and their origins will be discussed. 6) Plant CNSs are shorter and less frequent than mammalian CNSs, and no vertebrate-like ultra-conserved CNSs have yet been found.
The CNSs we find often make excellent PCR sites in noncoding regions of genome, and are expected to be present in all species less diverged than the CNSs themselves. For example, our rice-rice alphaCNSs make useful mapping and DNA extraction markers for each of the about 10,000 grasses.