Independent trait loss offer an amazing opportunity to study how the genome encodes a highly conserved trait. By identifying cis-regulatory elements which are eroded in species with an independent trait loss, we can identify regions which may encode the trait in question. In our study, we show that independently eroded transcription factor binding sites, which are otherwise highly conserved, are enriched for biological functions related to loss of hindlimbs in dolphin and manatee, degradation of vision in naked mole-rat and star-nosed mole, and the loss of external testes in white rhinoceros and Weddell seal. Below we present all conserved and eroded transcription factor binding sites for 57 placental mammals.
Mark J Berger, Aaron M Wenger, Harendra Guturu, Gill Bejerano; Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals, Nucleic Acids Research, , gky741, https://doi.org/10.1093/nar/gky741
Here we will recreate the set of independently eroded sites shared between dolphin and manatee. First we must download the eroded sites for our target species: turTru2.eroded.bed.gz, triMan1.eroded.bed.gz. We must also download the conserved sites for our outgroups species. Outgroup 1: panHod1.cons.bed.gz, bosTau7.cons.bed.gz, oviAri3.cons.bed.gz, capHir1.cons.bed.gz Outgroup 2: loxAfr3.cons.bed.gz, eleEdw1.cons.bed.gz Now we can use indep_eroded.py to generate the set of independently eroded sites.
python indep_eroded.py \ turTru2.eroded.bed.gz \ panHod1.cons.bed.gz,bosTau7.cons.bed.gz,oviAri3.cons.bed.gz,capHir1.cons.bed.gz \ triMan1.eroded.bed.gz \ loxAfr3.cons.bed.gz,eleEdw1.cons.bed.gz
|Species||UCSC genome assembly||Conserved TF Binding Sites||Eroded TF Binding Sites|