Primary data for the manuscript "Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution", by Roscito,Sameith,Parra et al. 2018. The directory contains - teguLizardGenome.fa The assembled genome of the tegu lizard in fasta format. - teguLizard.RM.out Repeat annotation of the tegu lizard genome in RepeatMasker out format. - tegu29wayAlignment.maf.gz The multiple genome alignment of 29 species with tegu lizard as the reference species. All species and assembly names are given in the Supplement, HLgekJap1 is the gecko assembly, HLpogVit1 is the dragon lizard assembly and HLtupMer3 refers to the tegu assembly. - mouse24wayAlignment.maf.gz The multiple genome alignment of 24 species with mouse (mm10 assembly) as the reference species. All species and assembly names are given in the Supplement. - teguLizard.genes.gp The final set of 23487 genes annotated in the tegu lizard in UCSC's genePred format. - teguLizard.genes.WithHumanOrthologs.gp The set of 16284 genes that have human orthologs in UCSC's genePred format. - teguCNEs.bed All 164422 CNEs used for the limb analysis in UCSC's bed format. Coordinates refer to the tegu genome. - mouseCNEs.bed All 491576 CNEs used for the eye analysis in UCSC's bed format. Coordinates refer to the mouse mm10 genome assembly. - limbStudy.CNE.global.percentID.txt The global percent identity values for all 164,423 CNEs used in the limb study. - limbStudy.CNE.local.percentID.txt The local percent identity values for all 164,423 CNEs used in the limb study. - limbStudy.simulatedCNE.global.percentID.txt The global percent identity values for all 38,438 CNEs used for simulating the null distribution of Z-scores. - eyeStudy.CNE.global.percentID.txt The global percent identity values for all 427,931 CNEs used in the eye study. - eyeStudy.CNE.local.percentID.txt The local percent identity values for all 427,931 CNEs used in the eye study. - limbStudy.tree.mod The phylogenetic tree used for obtaining PhastCons and GERP conserved elements and diverged CNEs - eyeStudy.tree.mod The phylogenetic tree used for obtaining PhastCons and GERP conserved elements and diverged CNEsh The 'sequencing' subdirectory contains all genome/mRNA/ATAC sequencing datasets and ATAC-seq peaks generated for this study with a separate README.txt