ArticleGenome research2019
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 58 citations in OpenAlex.
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- Patterns of chromosome evolution in ruminants.Molecular ecology · 2024Article
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- Comparative studies of X chromosomes in Cervidae family.Scientific reports · 2023Article
- Chromosomal conservatism vs chromosomal megaevolution: enigma of karyotypic evolution in Lepidoptera.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- Fixed Allele Differences Associated With the Centromere Reveal Chromosome Morphology and Rearrangements in a Reptile (Varanus acanthurus BOULENGER).Molecular biology and evolution · 2023Article
- An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics.Science advances · 2023Article
- syntenyPlotteR: a user-friendly R package to visualize genome synteny, ideal for both experienced and novice bioinformaticians.Bioinformatics advances · 2023Article
- Comparative genomic analysis of 5MFrontiers in plant science · 2023Article
- Evolution of the ancestral mammalian karyotype and syntenic regions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Temperature acclimation in hot-spring snakes and the convergence of cold response.Innovation (Cambridge (Mass.)) · 2022Article
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Authors and funding
20 authors at 13 institutions in 6 countries.
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Abstract
The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of
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