Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human

Authors

Svetlana A. Romanenko, Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia. rosa@mcb.nsc.ru.
Sergei F. Kliver, Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, Copenhagen, Denmark.
Natalia A. Serdyukova, Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.
Polina L. Perelman, Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.
Vladimir A. Trifonov, Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.
Andrei Seluanov, Department of Biology, University of Rochester, Rochester, NY, USA.
Vera Gorbunova, Department of Biology, University of Rochester, Rochester, NY, USA.
Jorge Azpurua, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA.
Jorge C. Pereira, Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.
Malcolm A. Ferguson-Smith, Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
Alexander S. Graphodatsky, Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.

Document Type

Journal Article

Publication Date

11-29-2023

Journal

Scientific reports

Volume

13

Issue

1

DOI

10.1038/s41598-023-46595-x

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.

APA Citation

Romanenko, Svetlana A.; Kliver, Sergei F.; Serdyukova, Natalia A.; Perelman, Polina L.; Trifonov, Vladimir A.; Seluanov, Andrei; Gorbunova, Vera; Azpurua, Jorge; Pereira, Jorge C.; Ferguson-Smith, Malcolm A.; and Graphodatsky, Alexander S., "Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human" (2023). GW Authored Works. Paper 3747.
https://hsrc.himmelfarb.gwu.edu/gwhpubs/3747

Department

Biochemistry and Molecular Medicine