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Abstract
Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.
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1 Russian Academy of Sciences, Siberian Branch, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (GRID:grid.4886.2) (ISNI:0000 0001 2192 9124)
2 The University of Copenhagen, Center for Evolutionary Hologenomics, The Globe Institute, Copenhagen, Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X)
3 Russian Academy of Sciences, Siberian Branch, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (GRID:grid.4886.2) (ISNI:0000 0001 2192 9124); Novosibirsk State University, Novosibirsk, Russia (GRID:grid.4605.7) (ISNI:0000 0001 2189 6553)
4 University of Rochester, Department of Biology, Rochester, USA (GRID:grid.16416.34) (ISNI:0000 0004 1936 9174)
5 The George Washington University, Department of Biochemistry and Molecular Medicine, Washington, USA (GRID:grid.253615.6) (ISNI:0000 0004 1936 9510)
6 University of Trás-os-Montes and Alto Douro, Animal and Veterinary Research Centre, Vila Real, Portugal (GRID:grid.12341.35) (ISNI:0000 0001 2182 1287); University of Cambridge, Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, Cambridge, UK (GRID:grid.5335.0) (ISNI:0000 0001 2188 5934)
7 University of Cambridge, Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, Cambridge, UK (GRID:grid.5335.0) (ISNI:0000 0001 2188 5934)