Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 114, Issue 27, Pages E5379-E5388Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1702012114
Keywords
chromosome evolution; ancestral genome reconstruction; genome rearrangements
Categories
Funding
- Ministry of Science, ICT & Future Planning of Korea [2014M3C9A3063544]
- Ministry of Education of Korea [2016R1D1A1B03930209]
- Rural Development Administration of Korea [PJ01040605]
- Biotechnology and Biological Sciences Research Council [BB/K008226/1, BB/J010170/1]
- Robert and Rosabel Osborne Endowment
- National Institutes of Health [HG007352]
- National Science Foundation [1054309, 1262575]
- Biotechnology and Biological Sciences Research Council [BB/J010170/1, BB/K008226/2, BB/J010170/2, BB/K008226/1] Funding Source: researchfish
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1619983] Funding Source: National Science Foundation
- National Research Foundation of Korea [2014M3C9A3063544, 2016R1D1A1B03930209] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)
- BBSRC [BB/J010170/2, BB/K008226/1, BB/K008226/2, BB/J010170/1] Funding Source: UKRI
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Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancestral chromosome reconstructions, we developed an algorithm (DESCHRAMBLER) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. The reconstructed chromosomes of the eutherian, boreoeutherian, and euarchontoglires ancestor each included >80% of the entire length of the human genome, whereas reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included >90% of human genome sequence. These high-coverage reconstructions permitted reliable identification of chromosomal rearrangements over similar to 105 My of eutherian evolution. Orangutan was found to have eight chromosomes that were completely conserved in homologous sequence order and orientation with the eutherian ancestor, the largest number for any species. Ruminant artiodactyls had the highest frequency of intrachromosomal rearrangements, and interchromosomal rearrangements dominated in murid rodents. A total of 162 chromosomal breakpoints in evolution of the eutherian ancestral genome to the human genome were identified; however, the rate of rearrangements was significantly lower (0.80/My) during the first similar to 60 My of eutherian evolution, then increased to greater than 2.0/My along the five primate lineages studied. Our results significantly expand knowledge of eutherian genome evolution and will facilitate greater understanding of the role of chromosome rearrangements in adaptation, speciation, and the etiology of inherited and spontaneously occurring diseases.
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