ArticleGigaScience2020
A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
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- Characterizing Physicochemical Selection in Protein Evolution with Property-Informed Models (PRIME).bioRxiv : the preprint server for biology · 2026Article
- Partitioned multi-MUM finding for scalable pangenomics with MumemtoM.Genome research · 2026Article
- MER57E3 transposable elements regulate gene expression in a human cell model of neural development.Genome biology · 2026Article
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- Phylogenomic Approaches to Study Adaptive Evolution in Mammals: From Aging to Aquatic Lifestyles.Annual review of genetics · 2025Review
- Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy.Cell genomics · 2025Article
- ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies.Genome research · 2025Article
- Metabolomics-Guided Genomic Comparisons Reveal Convergent Evolution of Hibernation Genes in Mammals.Molecular biology and evolution · 2025Article
- Evolution of cetacean-specific conserved non-coding elements suggests their role in the limb changes during secondary aquatic adaptation.BMC biology · 2025Article
- Partitioned Multi-MUM finding for scalable pangenomics.bioRxiv : the preprint server for biology · 2025Article
- Congenital Aphakia Associated With aClinical case reports · 2025Article
- Multi-level genomic convergence of secondary aquatic adaptation in marine mammals.Innovation (Cambridge (Mass.)) · 2025Article
- ERC 2.0 - evolutionary rate covariation update improves inference of functional interactions across large phylogenies.bioRxiv : the preprint server for biology · 2025Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundMultiple alignments of mammalian genomes have been the basis of many comparative genomic studies aiming at annotating genes, detecting regions under evolutionary constraint, and studying genome evolution. A key factor that affects the power of comparative analyses is the number of species included in a genome alignment.
resultsTo utilize the increased number of sequenced genomes and to provide an accessible resource for genomic studies, we generated a mammalian genome alignment comprising 120 species. We used this alignment and the CESAR method to provide protein-coding gene annotations for 119 non-human mammals. Furthermore, we illustrate the utility of this alignment by 2 exemplary 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% variable alignment columns. Furthermore, we show that the center regions of UCEs are generally most constrained. Second, we identified enhancer sequences that are only conserved in placental mammals. We found that these enhancers are significantly associated with placenta-related genes, suggesting that some of these enhancers may be involved in the evolution of placental mammal-specific aspects of the placenta.
conclusionThe 120-mammal alignment and all other data are available for analysis and visualization in a genome browser at https://genome-public.pks.mpg.de/and for download at https://bds.mpi-cbg.de/hillerlab/120MammalAlignment/.
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