A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers

摘要

Background: Multiple alignments of mammalian genomes have been the basis of many comparative genomic studiesaiming at annotating genes, detecting regions under evolutionary constraint, and studying genome evolution. A key factorthat affects the power of comparative analyses is the number of species included in a genome alignment. Results: To utilizethe increased number of sequenced genomes and to provide an accessible resource for genomic studies, we generated amammalian genome alignment comprising 120 species. We used this alignment and the CESAR method to provideprotein-coding gene annotations for 119 non-human mammals. Furthermore, we illustrate the utility of this alignment by 2exemplary analyses. First, we quantified how variable ultraconserved elements (UCEs) are among placental mammals.Leveraging the high taxonomic coverage in our alignment, we estimate that UCEs contain on average 4.7%–15.6% variablealignment columns. Furthermore, we show that the center regions of UCEs are generally most constrained. Second, weidentified enhancer sequences that are only conserved in placental mammals. We found that these enhancers aresignificantly associated with placenta-related genes, suggesting that some of these enhancers may be involved in theevolution of placental mammal-specific aspects of the placenta.