Reconstruction and evolutionary history of eutherian chromosomes

Kim, J; Farre Belmonte, M; Auvil, L S; Capitanu, B; Larkin, D M; Ma, J; Lewin, H A

Abstract

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.

Citation

Kim, J., Farre Belmonte, M., Auvil, L. S., Capitanu, B., Larkin, D. M., Ma, J., & Lewin, H. A. (2017). Reconstruction and evolutionary history of eutherian chromosomes. Proceedings of the National Academy of Sciences, 114(27), E5379-E5388. https://doi.org/10.1073/pnas.1702012114

• Journal Article Type: Article
• Acceptance Date: May 11, 2017
• Publication Date: Jul 3, 2017
• Deposit Date: Jul 5, 2017
• Publicly Available Date: Jul 1, 2018
• Journal: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• Print ISSN: 0027-8424
• Publisher: National Academy of Sciences
• Peer Reviewed: Peer Reviewed
• Volume: 114
• Issue: 27
• Pages: E5379-E5388
• DOI: https://doi.org/10.1073/pnas.1702012114
• Keywords: chromosome evolution; ancestral genome reconstruction; genome rearrangements
• Public URL: https://rvc-repository.worktribe.com/output/1391318
• Publisher URL: http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1702012114/-/DCSupplemental