TY - JOUR

T1 - Chromosome-length genome assembly of the stone marten (Martes foina, Mustelidae): A new view on one of the cornerstones in carnivore cytogenetics

AU - Tomarovsky, Andrey

AU - Khan, Ruqayya

AU - Dudchenko, Olga

AU - Totikov, Azamat

AU - Serdyukova, Natalia A

AU - Weisz, David

AU - Vorobieva, Nadejda V

AU - Bulyonkova, Tatiana

AU - Abramov, Alexei V

AU - Nie, Wenhui

AU - Wang, Jinhuan

AU - Romanenko, Svetlana A

AU - Proskuryakova, Anastasiya A

AU - Cherkasov, Nikolay

AU - Ferguson-Smith, Malcolm A

AU - Yang, Fengtang

AU - Balanovskaya, Elena

AU - Gilbert, M Thomas P

AU - Graphodatsky, Alexander S

AU - Aiden, Erez Lieberman

AU - Powell, Roger

AU - Koepfli, Klaus-Peter

AU - Perelman, Polina L

AU - Kliver, Sergei F.

N1 - © The Author(s) 2025. Published by Oxford University Press on behalf of The American Genetic Association. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.

PY - 2025/7/21

Y1 - 2025/7/21

N2 - The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n = 38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long runs of homozygosity require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large-scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.

AB - The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n = 38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long runs of homozygosity require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large-scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.

KW - Animals

KW - Male

KW - Mustelidae/genetics

KW - Genome

KW - Chromosome Painting

KW - Karyotype

KW - China

KW - Humans

KW - Cytogenetics

UR - https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=105011415267&origin=inward

UR - https://pubmed.ncbi.nlm.nih.gov/39879552/

U2 - 10.1093/jhered/esaf001

DO - 10.1093/jhered/esaf001

M3 - Article

C2 - 39879552

VL - 116

SP - 548

EP - 557

JO - The Journal of heredity

JF - The Journal of heredity

SN - 0022-1503

IS - 4

ER -