Evolution of the ancestral mammalian karyotype and syntenic regions
Authors
Damas, JoanaCorbo, Marco
Kim, Jaebum
Turner-Maier, Jason
Farré, Marta
Larkin, Denis M
Ryder, Oliver A
Steiner, Cynthia
Houck, Marlys L
Hall, Shaune
Shiue, Lily
Thomas, Stephen
Swale, Thomas
Daly, Mark
Korlach, Jonas
Uliano-Silva, Marcela
Mazzoni, Camila J
Birren, Bruce W
Genereux, Diane P
Johnson, Jeremy
Lindblad-Toh, Kerstin
Karlsson, Elinor K
Nweeia, Martin T
Johnson, Rebecca N
Lewin, Harris A
UMass Chan Affiliations
Program in Bioinformatics and Integrative BiologyProgram in Molecular Medicine
Document Type
Journal ArticlePublication Date
2022-09-26Keywords
ancestral genome reconstructionchromosome evolution
mammals
synteny conservation
topologically associating domains
Metadata
Show full item recordAbstract
Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.Source
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. Evolution of the ancestral mammalian karyotype and syntenic regions. Proc Natl Acad Sci U S A. 2022 Oct 4;119(40):e2209139119. doi: 10.1073/pnas.2209139119. Epub 2022 Sep 26. PMID: 36161960; PMCID: PMC9550189.DOI
10.1073/pnas.2209139119Permanent Link to this Item
http://hdl.handle.net/20.500.14038/51454PubMed ID
36161960Rights
Copyright © 2022 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).; Attribution 4.0 InternationalDistribution License
http://creativecommons.org/licenses/by/4.0/ae974a485f413a2113503eed53cd6c53
10.1073/pnas.2209139119
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