Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity

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Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity. / Houck, Marlys L.; Koepfli, Klaus-Peter; Hains, Taylor; Khan, Ruqayya; Charter, Suellen J.; Fronczek, Julie A.; Misuraca, Ann C.; Kliver, Sergei; Perelman, Polina L.; Beklemisheva, Violetta; Graphodatsky, Alexander; Luo, Shu-Jin; O'Brien, Stephen J.; Lim, Norman T.-L.; Chin, Jason S. C.; Guerra, Vanessa; Tamazian, Gaik; Omer, Arina; Weisz, David; Kaemmerer, Kenneth; Sturgeon, Ginger; Gaspard, Joseph; Hahn, Alicia; McDonough, Mark; Garcia-Treviño, Isabel; Gentry, Jordan; Coke, Rob L.; Janecka, Jan E.; Harrigan, Ryan J.; Tinsman, Jen; Smith, Thomas B.; Aiden, Erez Lieberman; Dudchenko, Olga.

In: Chromosome Research, Vol. 31, No. 2, 13, 2023.

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

Harvard

Houck, ML, Koepfli, K-P, Hains, T, Khan, R, Charter, SJ, Fronczek, JA, Misuraca, AC, Kliver, S, Perelman, PL, Beklemisheva, V, Graphodatsky, A, Luo, S-J, O'Brien, SJ, Lim, NT-L, Chin, JSC, Guerra, V, Tamazian, G, Omer, A, Weisz, D, Kaemmerer, K, Sturgeon, G, Gaspard, J, Hahn, A, McDonough, M, Garcia-Treviño, I, Gentry, J, Coke, RL, Janecka, JE, Harrigan, RJ, Tinsman, J, Smith, TB, Aiden, EL & Dudchenko, O 2023, 'Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity', Chromosome Research, vol. 31, no. 2, 13. https://doi.org/10.1007/s10577-023-09722-y

APA

Houck, M. L., Koepfli, K-P., Hains, T., Khan, R., Charter, S. J., Fronczek, J. A., Misuraca, A. C., Kliver, S., Perelman, P. L., Beklemisheva, V., Graphodatsky, A., Luo, S-J., O'Brien, S. J., Lim, N. T-L., Chin, J. S. C., Guerra, V., Tamazian, G., Omer, A., Weisz, D., ... Dudchenko, O. (2023). Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity. Chromosome Research, 31(2), [13]. https://doi.org/10.1007/s10577-023-09722-y

Vancouver

Houck ML, Koepfli K-P, Hains T, Khan R, Charter SJ, Fronczek JA et al. Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity. Chromosome Research. 2023;31(2). 13. https://doi.org/10.1007/s10577-023-09722-y

Author

Houck, Marlys L. ; Koepfli, Klaus-Peter ; Hains, Taylor ; Khan, Ruqayya ; Charter, Suellen J. ; Fronczek, Julie A. ; Misuraca, Ann C. ; Kliver, Sergei ; Perelman, Polina L. ; Beklemisheva, Violetta ; Graphodatsky, Alexander ; Luo, Shu-Jin ; O'Brien, Stephen J. ; Lim, Norman T.-L. ; Chin, Jason S. C. ; Guerra, Vanessa ; Tamazian, Gaik ; Omer, Arina ; Weisz, David ; Kaemmerer, Kenneth ; Sturgeon, Ginger ; Gaspard, Joseph ; Hahn, Alicia ; McDonough, Mark ; Garcia-Treviño, Isabel ; Gentry, Jordan ; Coke, Rob L. ; Janecka, Jan E. ; Harrigan, Ryan J. ; Tinsman, Jen ; Smith, Thomas B. ; Aiden, Erez Lieberman ; Dudchenko, Olga. / Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity. In: Chromosome Research. 2023 ; Vol. 31, No. 2.

Bibtex

@article{18174ad28cbb4de28ee0b0acc0be062f,
title = "Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity",
abstract = "We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.",
keywords = "chromosome number, genome assembly, karyotype, Phataginus tricuspis, Pholidota",
author = "Houck, {Marlys L.} and Klaus-Peter Koepfli and Taylor Hains and Ruqayya Khan and Charter, {Suellen J.} and Fronczek, {Julie A.} and Misuraca, {Ann C.} and Sergei Kliver and Perelman, {Polina L.} and Violetta Beklemisheva and Alexander Graphodatsky and Shu-Jin Luo and O'Brien, {Stephen J.} and Lim, {Norman T.-L.} and Chin, {Jason S. C.} and Vanessa Guerra and Gaik Tamazian and Arina Omer and David Weisz and Kenneth Kaemmerer and Ginger Sturgeon and Joseph Gaspard and Alicia Hahn and Mark McDonough and Isabel Garcia-Trevi{\~n}o and Jordan Gentry and Coke, {Rob L.} and Janecka, {Jan E.} and Harrigan, {Ryan J.} and Jen Tinsman and Smith, {Thomas B.} and Aiden, {Erez Lieberman} and Olga Dudchenko",
note = "Publisher Copyright: {\textcopyright} 2023. The Author(s), under exclusive licence to Springer Nature B.V.",
year = "2023",
doi = "10.1007/s10577-023-09722-y",
language = "English",
volume = "31",
journal = "Chromosome Research",
issn = "0967-3849",
publisher = "Springer",
number = "2",

}

RIS

TY - JOUR

T1 - Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity

AU - Houck, Marlys L.

AU - Koepfli, Klaus-Peter

AU - Hains, Taylor

AU - Khan, Ruqayya

AU - Charter, Suellen J.

AU - Fronczek, Julie A.

AU - Misuraca, Ann C.

AU - Kliver, Sergei

AU - Perelman, Polina L.

AU - Beklemisheva, Violetta

AU - Graphodatsky, Alexander

AU - Luo, Shu-Jin

AU - O'Brien, Stephen J.

AU - Lim, Norman T.-L.

AU - Chin, Jason S. C.

AU - Guerra, Vanessa

AU - Tamazian, Gaik

AU - Omer, Arina

AU - Weisz, David

AU - Kaemmerer, Kenneth

AU - Sturgeon, Ginger

AU - Gaspard, Joseph

AU - Hahn, Alicia

AU - McDonough, Mark

AU - Garcia-Treviño, Isabel

AU - Gentry, Jordan

AU - Coke, Rob L.

AU - Janecka, Jan E.

AU - Harrigan, Ryan J.

AU - Tinsman, Jen

AU - Smith, Thomas B.

AU - Aiden, Erez Lieberman

AU - Dudchenko, Olga

N1 - Publisher Copyright: © 2023. The Author(s), under exclusive licence to Springer Nature B.V.

PY - 2023

Y1 - 2023

N2 - We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.

AB - We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.

KW - chromosome number

KW - genome assembly

KW - karyotype

KW - Phataginus tricuspis

KW - Pholidota

U2 - 10.1007/s10577-023-09722-y

DO - 10.1007/s10577-023-09722-y

M3 - Journal article

C2 - 37043058

AN - SCOPUS:85152489194

VL - 31

JO - Chromosome Research

JF - Chromosome Research

SN - 0967-3849

IS - 2

M1 - 13

ER -

ID: 344797118