Identification and characterization of <i>de novo</i> genes in human and chimpanzee.

<p><b>a)</b> Simplified phylogenetic tree indicating the nine species considered in this study. In all species we had RNA-Seq data from several tissues. Chimpanzee, human, macaque and mouse were the species for which we performed strand-specific deep polyA+ RNA sequencing. We indicate the branches in which <i>de novo</i> genes were defined, together with the number of genes. <b>b)</b> Categories of transcripts in <i>de novo</i> genes based on genomic location. Intergenic, transcripts that do not overlap any other gene; Overlapping antisense, transcripts that overlap exons from other genes in the opposite strand; Overlapping intronic, transcripts that overlap introns from other genes in the opposite strand, with no exonic overlap. <b>c)</b> Classification of <i>de novo</i> genes based on existing evidence in databases. Annotated; genes classified as annotated in Ensembl v.75; EST/nr; non-annotated genes with BLAST hits (10⁻⁴) to expressed sequence tags (EST) and/or non-redundant protein (nr) sequences in the same species. Novel; rest of genes. <b>d)</b> Patterns of gene expression in four tissues. Brain refers to frontal cortex. Transcripts with FPKM > 0 in a tissue are considered as expressed in that tissue. In red boxes, fraction of transcripts whose expression is restricted to that tissue (τ > 0.85, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005721#sec009" target="_blank">Methods</a>). Chimp conserved, transcripts assembled in chimpanzee not classified as <i>de novo</i>. Human conserved, transcripts assembled in human not classified as <i>de novo</i>. <b>e)</b> Number of testis GTEx samples with expression of <i>de novo</i> and conserved genes. We considered all annotated genes with FPKM > 0 in at least one testis sample. Conserved, genes sampled from the total pool of annotated genes analyzed in GTEx with the same distribution of FPKM values than in annotated <i>de novo</i> genes (n = 200).