Genomic mapping and molecular processes Christian Gautier, Vincent Navratil, Christelle Melo de Lima LBBE, Universit Lyon I, 43 bd 11 novembre,69622 Villeurbanne Cedex, FRANCE Abstract This paper describe both management and analysis of genomic mapping data. A UML representation of both vertebrates genome maps and evolutionary relationships between gene is presented. Statisti- cal analysis has focused on isochore organisation, subtitution rate and skew. Natural selection versus mutational bias is discussed. Keywords:Genomic mapping, evolution 1 Introduction Gene density, gene structure as well as genomic sequence statistical properties vary along genomes and define regions that are more or less homoge- neous. These regions interact with three levels of biological constraints: i) genetic information includ- ing genes, regulatory elements, ...; ii) the manage- ment process of this information (transcription or replication units, recombination process, ...); iii) the spatial organisation of the genomic DNA with the different packaging level of chromatin (nucleosomes and higher order organisation). An important step in understanding the functioning of genomes is to associate statistical properties of sequences to each of these biological constraints. However this anal- ysis must take into account evolutionary processes that have generated and that maintain these asso- ciations. Genomic patterns so results from a combi- nation of several levels of constraints, natural selec- tion and mutational bias. Inferring processes from patterns is a very complex task, this paper tries to show that taking into account spatial organisation could be of great help in genomic sequence analy- sis. This strategy needs developping new method- ological tools both to manage and to analyse data. In this paper we will mainly focus on data base management in wich we are embedded from several years [1]. However some reference to statistical de- velopments will be made. Prokaryotic and eukaryotic genomes have quite different behaviors relatively to spatial patterns. We will present separatly these two groups of organ- isms and will focuse for eucaryotes on vertebrates. 2 Procaryotic genome pat- terns Complete procaryotic genome has been the first ho- mogeneous unit describe [2] and its discussion take always an important role in the debate between mu- tation bias versus selection in genome patterning. Sueka, as soon as in xxxx, determined experimen- tally the G+C content of bacterial genomes. It ap- pears that those genomes show a very large range of G+C content. This raises the debate between two hypothesis: i) G+C content is linked to the fitness of the organism and its level results from a natural selection process; ii) the G+C content range inside bacteria results from a varability of the mutational bias. So the G+C content variability takes place in- side the neutralist vs selectionist debate. Due to the fact that G.C link is stronger than A.T link, it has been postulated that optimal growth temperature (T opt )determine selection pressure acting on G+C content. Correlation studies between T opt and G+C content have ruled out this hypothesis. Sueoka pro- pose then his hypothesis of neutral modification of the replication apparatus implying variation of mu- tational bias. More recent studies [3] have precised relationships between temperature and G+C con- tent. If no relation exists between genomic G+C content and T opt , T opt is correlated to the G+C content of genome regions coding for helix part of ribosomal RNA. This shows that probably two evo- 1