On the Universal Random-Like Structure of Genomes

FRANÇOIS SERRA; VERÓNICA BECHER; HERNAN DOPAZO

Barcelona

Jornada; XI Jornadas de Bioinformática; 2012

Most biologists agree that the genomes of complex organisms require a higher number of genetic directives, hence, larger genomes [1]. Lynch and Conery hypothesized that genome size and its complexity inevitable increased as the consequence of population size reduction in linages [2]. Definitions of biological complexity have not been completely successful because they work well just for specific properties [3]. In contrast, formalizations of complexity at the genome level have received fewer objections [4,5]. These studies however, focused on specific species, and used methods that involve genome fragmentation; hence, those results are local to the analyzed DNA fragments. Here we ask for the global combinatorial structure of DNA in biodiversity. Is there a common law in the DNA sequences of all genomes? In this work we tested the hypothesis that there is a common combinatorial structure of DNA in all genomes. Our hypothesis is that there is a random-like structure of DNA along all diversity of life. To test it, we define a complexity measure based on a classical method used in data compression [6] and applicable to arbitrarily large sequences introducing no fragmentation. The method detects regularities due to repeats of any length, at any distance, and other structural correlations. As the main result we report that the ratio of genome complexity to size remained almost maximal and unchanged along six orders of magnitude in genome size, covering all biological diversity. We observe a uniform complexity increases with genome size for phages, bacteria, unicellular eukaryotes, fungi, plants, and animals. Major deviations from maximal genome complexity correspond to polyploid species. Diploidization [7] -the process by which a polyploid genome turns into a diploid one- guaranties the return to almost maximum complexity. We formulate two general hypotheses: 1- almost maximal combinatorial structure of DNA sequence is a common characteristic of genomes throughout biological diversity; 2- increases in the combinatorial complexity of DNA only occur by mechanisms of genome amplification, and subsequent accumulation of DNA sequence mutations, transpositions and/or deletions of genetic material. Our hypothesis can be falsified if a single recent polyploid genome with a random-like DNA structure is found; or if a non-polyploid genome shows a non-random DNA structure.