Research output: Contribution to journal › Article › peer-review
Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). / Kliver, Sergei; Houck, Marlys L; Perelman, Polina L et al.
In: The Journal of heredity, Vol. 114, No. 5, esad035, 01.09.2023, p. 539-548.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)
AU - Kliver, Sergei
AU - Houck, Marlys L
AU - Perelman, Polina L
AU - Totikov, Azamat
AU - Tomarovsky, Andrei
AU - Dudchenko, Olga
AU - Omer, Arina D
AU - Colaric, Zane
AU - Weisz, David
AU - Aiden, Erez Lieberman
AU - Chan, Saki
AU - Hastie, Alex
AU - Komissarov, Aleksey
AU - Ryder, Oliver A
AU - Graphodatsky, Alexander
AU - Johnson, Warren E
AU - Maldonado, Jesús E
AU - Pukazhenthi, Budhan S
AU - Marinari, Paul E
AU - Wildt, David E
AU - Koepfli, Klaus-Peter
N1 - The sequencing and assembly of the black-footed ferret genome were funded by a grant from the Smithsonian Institution Competitive Pell Grants Program in Science awarded to WEJ, K-PK, JEM, PEM, BSP, and DEW. This study was also partly funded by the RSF grant no. 19-14-00034-P. SK was funded from Carlsbergfondet Research Infrastructure Grant CF22-0680. ELA was supported by the Welch Foundation (Q-1866), a McNair Medical Institute Scholar Award, an NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375), a US-Israel Binational Science Foundation Award (2019276), the Behavioral Plasticity Research Institute (NSF DBI-2021795), NSF Physics Frontiers Center Award (NSF PHY-2019745 and PHY-2210291), and an NIH CEGS (RM1HG011016-01A1). © The Author(s) 2023. Published by Oxford University Press on behalf of The American Genetic Association. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
PY - 2023/9/1
Y1 - 2023/9/1
N2 - The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex-situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 Kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million years ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.
AB - The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex-situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 Kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million years ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.
KW - Animals
KW - Endangered Species
KW - Ferrets/genetics
KW - Fertility
KW - Karyotype
KW - Karyotyping
KW - Male
UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85168787369&origin=inward&txGid=e258aec76bc13d2c16ec40e1e3b2a806
UR - https://www.mendeley.com/catalogue/21535d09-56d7-30b0-a44d-80f128d63616/
U2 - 10.1093/jhered/esad035
DO - 10.1093/jhered/esad035
M3 - Article
C2 - 37249392
VL - 114
SP - 539
EP - 548
JO - The Journal of heredity
JF - The Journal of heredity
SN - 0022-1503
IS - 5
M1 - esad035
ER -
ID: 50661298