Damas J, Corbo M, Kim J, Turner-Maier J, Farré M, Larkin DM, Ryder OA, Steiner C, Houck ML, Hall S, Shiue L, Thomas S, Swale T, Daly M, Korlach J, Uliano-Silva M, Mazzoni CJ, Birren BW, Genereux DP, Johnson J, Lindblad-Toh K, Karlsson EK, Nweeia MT, Johnson RN; Zoonomia Consortium; Lewin HA.

Proc Natl Acad Sci U S A. 2022 Oct 4;119(40):e2209139119. doi: 10.1073/pnas.2209139119

Evolution of the ancestral mammalian karyotype and syntenic regions.

Analyses the number of breakpoints between nodes of the phylogenetic tree, thanks to ancestral genome reconstruction. “2 extant mammals (Dataset S1), representing all 19 eutherian, 3 marsupial, and the monotreme orders, were used to reconstruct ancestral karyotypes at 16 nodes of the mammalian phylogeny” “We used DESCHRAMBLER to generate reconstructed ancestral chromosome fragments (RACFs) for each of 16 mammalian ancestors at 300-kbp syntenic fragment (SF) resolution” “The reconstructed mammalian ancestor karyotype has 19 autosomes plus X, except for the cattle genome-based reconstruction, which has two fewer chromosomes and the lowest total reconstruction length” “The differences between the mammalian and therian (n = 17 + X) ancestors’ chromosomes resulted from 96 chromosomal rearrangements over 18 My.” “The eutherian ancestor (n = 19 + X) is the most recent common ancestor of the three lineages represented by the reference genomes. Its karyotype evolved from that of the therian ancestor as a result of 124 chromosomal rearrangements over 53 My.” “We identified 323, 262, and 257 EBRs that occurred along the lineage from the mammalian ancestor to the human, sloth, and cattle genomes, respectively” “Inversions were most frequent, accounting for 76 to 85% of all rearrangements identified for each lineage” “The highest number of interchromosomal rearrangements (i.e., fissions and fusions) was observed on the branch from the therian to the eutherian ancestor (n = 30)” “We observed that 9 of 14 small MAMs have 1:1 orthology to chicken chromosomes (GGA) and reconstructed chromosomes of the avian and amniote ancestors” “EBRs were found to have a significantly higher density of repeats”