Biology Faculty Articles


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


Marlys L. Houck, San Diego Zoo Wildlife Alliance
Klaus-Peter Koepfli, George Mason University; Smithsonian’s National Zoo and Conservation Biology Institute; ITMO University
Taylor Hains, University of Chicago
Ruqayya Khan, Baylor College of Medicine
Suellen J. Charter, San Diego Zoo Wildlife Alliance
Julie A. Fronczek, San Diego Zoo Wildlife Alliance
Ann C. Misuraca, San Diego Zoo Wildlife Alliance
Sergei Kliver, The University of Copenhagen
Polina L. Perelman, Institute of Molecular and Cellular Biology SB RAS
Violetta R. Beklemisheva, Institute of Molecular and Cellular Biology SB RAS
Alexander Graphodatsky, Institute of Molecular and Cellular Biology SB RAS
Shu-Jin Luo, Peking University
Stephen J. O’Brien, ITMO University; Nova Southeastern UniversityFollow
Norman T.-L. Lim, Nanyang Technological University
Jason S. C. Chin, Taipei Zoo
Vanessa Guerra, Simon Fraser University; Smithsonian Institution
Gaik Tamazian, Peter the Great Saint Petersburg Polytechnic University
Arina Omer, Baylor College of Medicine
David Weisz, Baylor College of Medicine
Kenneth Kaemmerer, Pittsburgh Zoo & Aquarium
Ginger Sturgeon, Pittsburgh Zoo & Aquarium
Joseph Gaspard, Pittsburgh Zoo & Aquarium
Alicia Hahn, Pittsburgh Zoo & Aquarium
Mark McDonough, Pittsburgh Zoo & Aquarium
Isabel Garcia-Treviño, San Antonio Zoo
Jordan Gentry, San Antonio Zoo
Rob L. Coke, San Antonio Zoo
Jan E. Janecka, Duquesne University
Ryan J. Harrigan, University of California
Jen Tinsman, University of California
Thomas B. Smith, University of California
Erez Lieberman Aiden, Baylor College of Medicine; Rice University; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT)
Olga Dudchenko, Baylor College of Medicine; Rice University

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Publication Date


Publication Title

Chromosome Research


chromosome number, karyotype, Pholidota, Phataginus tricuspis, genome assembly






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.


Work was supported by grants from the National Geographic Society (NGS-418C-18) and US Gov. INLEC (S-INLEC-17-GR-1006). E.L.A. 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), an NSF Physics Frontiers Center Award (NSF PHY-2019745), and an NIH CEGS (RM1HG011016-01A1). A.S. Graphodatsky, P.L. Perelman, and V.R. Beklemisheva were supported by the Russian Science Foundation (Grant No. 19–14-00034p to A.S.G.). G. Tamazian was supported by Peter the Great St. Petersburg Polytechnic University in the framework of the Russian Federation’s Priority 2030 Strategic Academic Leadership Programme (Agreement 075–15-2021–1333).

Ethical approval The blood sample from the white-bellied pangolin, Jaziri, was collected opportunistically in April 2019 during a routine veterinary examination by the veterinary staf at the Pittsburgh Zoo & Aquarium, following all required and standard animal handling protocols and with approval by the Pittsburgh Zoo & Aquarium institutional animal care and use committee.

© The Author(s), under exclusive licence to Springer Nature B.V. 2023



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