Multiple species analysis of large genomic regions in Drosophila . B.D. Pfeiffer ¹, C. Bergman ¹, R. Hoskins ¹, B. Berman ², K. Wan ¹, M. Stapleton ¹, R. George ¹, M. Champe ¹, B. Kronmiller ¹, G. Rubin ³, S.E. Celniker ¹. 1) Drosophila Genome Project, Lawrence Berkeley Natl Lab, Berkeley, CA; 2) Department of Molecular and Cell Biology, University of California, Berkeley, CA; 3) University of California, Berkeley and HHMI, Washington, DC.

   We are using large scale comparative genomics to investigate conservation in both coding and non-coding regions of the Drosophila genome. For this study, we have chosen to sequence eight homologous regions each spanning approximately 37 kb from D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis . These species have diverged from D. melanogaster by 15, 46, 53, and 60 million years, respectively. Using AVID [N. Bray, A. Fabrikant, J. Lord, J. Schwartz, I. Dubchak, and L. Pachter ((in prep.)], an alignment algorithm, and VISTA, a visualization tool, (http://www-gsd.lbl.gov/vista), we have analyzed the level of synteny and rearrangements within each of the eight regions. Since there is no standard tool for multiple alignments, in addition to AVID, we are evaluating two other alignments tools, Lamark [A. Ogurtsov, S. Shabalina and A. Kondarashov (unpublished)], and DiAlign [Morgenstern 2000]). Using the optimum alignments, we will present the percent identities of coding and non-coding regions, the base composition and codon bias for each species. A major goal of this project is to evaluate the levels of conservation in functionally characterized cis-regulatory regions as a training set for future whole genome comparative sequence analysis. We are studying eight genes apterous, even-skipped, fushi tarazu, twist, and the four rhodopsins whose cis-regulatory sequences have been well defined in Drosophila melanogaster . We are examining conservation of the cis-regulatory regions both at the level of known enhancers and known binding sites. In addition, we have identified clustered transcription factor binding sites within the homolgous cis-regulatory regions of eve using CIS-ANALYST (B. Berman, 2001).