Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia.
Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.
Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.|Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
Laia
L
Capilla
Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.|Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico.
Rosa Ana
RA
Sánchez-Guillén
Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico.
Marta
M
Farré
Department of Comparative Biomedical Sciences, The Royal Veterinary College, London, UK.|Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain.
Andreu
A
Paytuví-Gallart
Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
Roberto
R
Malinverni
Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
Jacint
J
Ventura
Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico.
Denis M
DM
Larkin
Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.|Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain.
Aurora
A
Ruiz-Herrera
D000818:Animals; D042002:Chromatin Assembly and Disassembly; D056905:Chromosome Breakpoints; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics; D011995:Recombination, Genetic; D012377:Rodentia / Q000235:genetics*
rodents; evolutionary breakpoints; recombination; KRAB genes; epigenome; lamina associated domains