Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). / Kliver, Sergei; Houck, Marlys L.; Perelman, Polina L.; Totikov, Azamat; Tomarovsky, Andrei; Dudchenko, Olga; Omer, Arina D.; Colaric, Zane; Weisz, David; Aiden, Erez Lieberman; Chan, Saki; Hastie, Alex; Komissarov, Aleksey; Ryder, Oliver A.; Graphodatsky, Alexander; Johnson, Warren E.; Maldonado, Jesús E.; Pukazhenthi, Budhan S.; Marinari, Paul E.; Wildt, David E.; Koepfli, Klaus-Peter.

In: Journal of Heredity, Vol. 114, No. 5, 2023, p. 539-548.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Kliver, S, Houck, ML, Perelman, PL, Totikov, A, Tomarovsky, A, Dudchenko, O, Omer, AD, Colaric, Z, Weisz, D, Aiden, EL, Chan, S, Hastie, A, Komissarov, A, Ryder, OA, Graphodatsky, A, Johnson, WE, Maldonado, JE, Pukazhenthi, BS, Marinari, PE, Wildt, DE & Koepfli, K-P 2023, 'Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)', Journal of Heredity, vol. 114, no. 5, pp. 539-548. https://doi.org/10.1093/jhered/esad035

APA

Kliver, S., Houck, M. L., Perelman, P. L., Totikov, A., Tomarovsky, A., Dudchenko, O., Omer, A. D., Colaric, Z., Weisz, D., Aiden, E. L., Chan, S., Hastie, A., Komissarov, A., Ryder, O. A., Graphodatsky, A., Johnson, W. E., Maldonado, J. E., Pukazhenthi, B. S., Marinari, P. E., ... Koepfli, K-P. (2023). Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). Journal of Heredity, 114(5), 539-548. https://doi.org/10.1093/jhered/esad035

Vancouver

Kliver S, Houck ML, Perelman PL, Totikov A, Tomarovsky A, Dudchenko O et al. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). Journal of Heredity. 2023;114(5):539-548. https://doi.org/10.1093/jhered/esad035

Author

Kliver, Sergei ; Houck, Marlys L. ; Perelman, Polina L. ; Totikov, Azamat ; Tomarovsky, Andrei ; Dudchenko, Olga ; Omer, Arina D. ; Colaric, Zane ; Weisz, David ; Aiden, Erez Lieberman ; Chan, Saki ; Hastie, Alex ; Komissarov, Aleksey ; Ryder, Oliver A. ; Graphodatsky, Alexander ; Johnson, Warren E. ; Maldonado, Jesús E. ; Pukazhenthi, Budhan S. ; Marinari, Paul E. ; Wildt, David E. ; Koepfli, Klaus-Peter. / Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). In: Journal of Heredity. 2023 ; Vol. 114, No. 5. pp. 539-548.

Bibtex

@article{bd431546fc524d21b4dcdce0d2201130,
title = "Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)",
abstract = "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.",
author = "Sergei Kliver and Houck, {Marlys L.} and Perelman, {Polina L.} and Azamat Totikov and Andrei Tomarovsky and Olga Dudchenko and Omer, {Arina D.} and Zane Colaric and David Weisz and Aiden, {Erez Lieberman} and Saki Chan and Alex Hastie and Aleksey Komissarov and Ryder, {Oliver A.} and Alexander Graphodatsky and Johnson, {Warren E.} and Maldonado, {Jes{\'u}s E.} and Pukazhenthi, {Budhan S.} and Marinari, {Paul E.} and Wildt, {David E.} and Klaus-Peter Koepfli",
note = "{\textcopyright} 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.",
year = "2023",
doi = "10.1093/jhered/esad035",
language = "English",
volume = "114",
pages = "539--548",
journal = "Journal of Heredity",
issn = "0022-1503",
publisher = "Oxford University Press",
number = "5",

}

RIS

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 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

Y1 - 2023

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.

U2 - 10.1093/jhered/esad035

DO - 10.1093/jhered/esad035

M3 - Journal article

C2 - 37249392

VL - 114

SP - 539

EP - 548

JO - Journal of Heredity

JF - Journal of Heredity

SN - 0022-1503

IS - 5

ER -

ID: 361590143