Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories
Open accessAbstract
The persistence of large blocks of homologous synteny and a high frequency of breakpoint reuse are distinctive features of mammalian chromosomes that are not well understood in evolutionary terms. To gain a better understanding of the evolutionary forces that affect genome architecture, synteny relationships among 10 amniotes (human, chimp, macaque, rat, mouse, pig, cattle, dog, opossum, and chicken) were compared at <1 human-Mbp resolution. Homologous synteny blocks (HSBs; N = 2233) and chromosome evolutionary breakpoint regions (EBRs; N = 1064) were identified from pairwise comparisons of all genomes. Analysis of the size distribution of HSBs shared in all 10 species' chromosomes (msHSBs) identified three (>20 Mbp) that are larger than expected by chance. Gene network analysis of msHSBs >3 human-Mbp and EBRs <1 Mbp demonstrated that msHSBs are significantly enriched for genes involved in development of the central nervous and other organ systems, whereas EBRs are enriched for genes associated with adaptive functions. In addition, we found EBRs are significantly enriched for structural variations (segmental duplications, copy number variants, and indels), retrotransposed and zinc finger genes, and single nucleotide polymorphisms. These results demonstrate that chromosome breakage in evolution is nonrandom and that HSBs and EBRs are evolving in distinctly different ways. We suggest that natural selection acts on the genome to maintain combinations of genes and their regulatory elements that are essential to fundamental processes of amniote development and biological organization. Furthermore, EBRs may be used extensively to generate new genetic variation and novel combinations of genes and regulatory elements that contribute to adaptive phenotypes.
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Using the human genome as an outgroup, 207 conserved ancestral homologous synteny blocks (aHSBs) were reconstructed, covering 2.51 Gb (94%) of the yak genome.
“Using the human genome as an outgroup, we reconstructed 207 conserved ancestral homologous synteny blocks (aHSBs) 16 covering 2.51 Gb (94%) of the yak genome.”
From The yak genome and adaptation to life at high altitude (2012) · cites this paper as [16]
The Identification of HSBs section describes defining homologous synteny blocks using the human genome as a reference, supporting the methodological connection. It does not describe human as an outgroup or report 207 ancestral blocks covering 2.51 Gb (94%) of a yak genome; yak is not among the genomes analyzed. No page number is available in our copy. (LLM, conf=0.88)
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The yak genome and adaptation to life at high altitude
Qiu, Q., Zhang, G., Ma, T., Qian, W., Wang, J., Ye, Z., Cao, C., Hu, Q., Kim, J., Larkin, D. M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2343 · Cited by 971 · see citing works
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Self-citationChromosome reciprocal translocations have accompanied subspecies evolution in bananas
Martin, G., Baurens, F., Hervouet, C., Salmon, F., Delos, J., Labadie, K., Perdereau, A., Mournet, P., Blois, L., Dupouy, M., et al. (2020) · The Plant Journal · doi:10.1111/tpj.15031 · Cited by 66 · see citing works
- Authors
- Larkin, D. M., Pape, G., Donthu, R., Auvil, L., Welge, M., & Lewin, H. A.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-04-02
- Volume
- 19
- Issue
- 5
- Pages
- 770-777
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2675965
- OpenAlex
- W2108876013
- Cited by
- 184
- References
- 39
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 5 · 2023: 11 · 2022: 11 · 2021: 5 · 2020: 8 · 2019: 14 · 2018: 12 · 2017: 15 · 2016: 12 · 2015: 13 · 2014: 13 · 2013: 5 · 2012: 13
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- RVC Research Online (Royal Veterinary College) (submittedVersion, cc-by)
- Funders
- U.S. Department of Agriculture
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- structural variants, segmental duplication, copy number variation, retrotransposition, zinc finger genes, single nucleotide polymorphisms, gene network analysis, adaptive evolution
- MeSH terms
- Animals, Humans, Models, Genetic, Selection, Genetic, Genome, Evolution, Molecular, Chromosome Breakage, Gene Duplication, Synteny, Chromosomes, Mammalian
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