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Reconstruction and evolutionary history of eutherian chromosomes

Kim, Jaebum, Farré, Marta, Auvil, Loretta, Capitanu, Boris, Larkin, Denis M, Ma, Jian, Lewin, Harris A (2017) Reconstruction and evolutionary history of eutherian chromosomes. Proceedings of the National Academy of Sciences of the United States of America, 114 (27). pp. 5379-5388. ISSN 1091-6490. E-ISSN 1091-6490. (doi:10.1073/pnas.1702012114) (KAR id:70465)

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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 ?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 ?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.

Item Type: Article
DOI/Identification number: 10.1073/pnas.1702012114
Uncontrolled keywords: chromosome evolution, ancestral genome reconstruction, genome rearrangements, School of Biosciences
Subjects: Q Science > QR Microbiology
Divisions: Faculties > Sciences > School of Biosciences
Depositing User: Marta Farre Belmonte
Date Deposited: 29 Nov 2018 17:19 UTC
Last Modified: 04 Feb 2020 11:40 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/70465 (The current URI for this page, for reference purposes)
Farré, Marta: https://orcid.org/0000-0001-9170-5767
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