TY - JOUR

T1 - Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human

AU - Romanenko, Svetlana A

AU - Kliver, Sergei F

AU - Serdyukova, Natalia A

AU - Perelman, Polina L

AU - Trifonov, Vladimir A

AU - Seluanov, Andrei

AU - Gorbunova, Vera

AU - Azpurua, Jorge

AU - Pereira, Jorge C

AU - Ferguson-Smith, Malcolm A

AU - Graphodatsky, Alexander S

N1 - VG and AS are supported by grants from the US National Institutes of Health. This research was funded by Russian Science Foundation grant No 19-14-00034-П (ASG). The research was completed using equipment (materials) of the Core Facilities Centre “Cryobank of cell cultures” Institute of Molecular and Cellular Biology SB RAS (Novosibirsk, Russia). © 2023. The Author(s). Публикация для корректировки.

PY - 2023/11/29

Y1 - 2023/11/29

N2 - 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.

AB - 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.

KW - Humans

KW - Guinea Pigs

KW - Animals

KW - Synteny

KW - In Situ Hybridization, Fluorescence

KW - Genome

KW - Karyotype

KW - Mole Rats/genetics

U2 - 10.1038/s41598-023-46595-x

DO - 10.1038/s41598-023-46595-x

M3 - Article

C2 - 38030702

VL - 13

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

M1 - 21055

ER -