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.
Highlights
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 reconstruction of ancestral chromosomes, the human genome was used as the reference for alignments because of the relative quality of the assembly, and because we focused reconstructions on the evolution of lineages leading to human
The ancestral reconstructions far surpassed the quality of previous map and sequence-based reconstructions in terms of the number of descendant species included, coverage of ancestor genomes relative to the human genome, and the number of ancestors in the evolutionary path to the human genome [3, 4], providing novel insights into eutherian and primate genome evolution
Summary
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. A distinct advantage of resolving EBRs at high resolution is that sequence features within them can be interrogated for genes that may be associated with lineage-specific phenotypes This is an important motivation for creating finerscale ancestral chromosome reconstructions [10, 12, 13]. Several algorithms have been developed to reconstruct the order and orientation of syntenic fragments (SFs) in common ancestors by using DNA sequence-level syntenic relationships among genomes of extant species. Our results provide an evolutionary basis for comparison of genome organization of all eutherians, and for revealing the genomic origins of lineage-specific adaptations
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