Animals actively use at least half of the genome

10 One central goal of genome biology is to understand how the usage of the genome differs between 11 organisms. Our knowledge of genome composition, needed for downstream inferences, is critically 12 dependent on gene annotations, yet problems associated with gene annotation and assembly errors are 13 usually ignored in comparative genomics. Here we analyze the genomes of 68 species across all animal 14 groups and some single-cell eukaryotes for general trends in genome usage and composition, taking into 15 account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to 16 intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by 17 increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that 18 the majority of published genomes of non-model organisms are underannotated and consequently omit 19 substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our 20 results also indicate that most animals transcribe half or more of their genomes arguing against differences 21 in genome usage between animal groups, and also suggesting that the transcribed portion is more 22 dependent on genome size than previously thought. 23