Genome assemblies and RNA-seq. (A) Bayesian phylogenetic tree of 20 sequenced Drosophila species (four letter abbreviations). All nodes are supported by 100% posterior probabilities. Scale bar indicates phylogenetic distance in substitutions per site (ss). Previously (italics) and newly assembled (bold italics) genomes, and those with supporting RNA-seq data (asterisk) are indicated. (B) Scatterplot showing alignment versus phylogenetic distance from D. melanogaster (linear trendline in red). (C) Heatmap and hierarchical clustering of expression values for 3223 first coding exons from the indicated samples. Adult ovary (dark red) and testis (dark blue) included developing germ cells and somatic gonadal cells and internal reproductive tracts derived from the genital disc. Females (pink) and males (light blue) were whole adults, embryos were unsexed, heads were from adults, and carcasses were all adult tissues remaining after removal of the gonads and internal reproductive tract. RPKM scale is shown for 15 species. The distance scale for hierarchical leaves was arbitrary. (D) Sequencing depth by species. A limited number of RNA-seq reads from heads (20.5 million reads for D. melanogaster, 28.4 million reads for D. pseudoobscura, and 51.6 million reads for D. mojavensis) were previously published (Graveley et al. 2011). The remaining reads are reported here for the first time. (E) The number of each element type from the modENCODE version 2 (MDv2) annotation. We examined the conserved sequence and expression characteristics of all such elements. For purposes of analysis, exons with both UTR and CDS sequences were split.
