Biology Faculty Articles
Title
Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity
Document Type
Article
Publication Date
4-12-2023
Publication Title
Chromosome Research
Keywords
chromosome number, karyotype, Pholidota, Phataginus tricuspis, genome assembly
ISSN
1573-6849
Issue/No.
13
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.
NSUWorks Citation
Houck, Marlys L.; Klaus-Peter Koepfli; Taylor Hains; Ruqayya Khan; Suellen J. Charter; Julie A. Fronczek; Ann C. Misuraca; Sergei Kliver; Polina L. Perelman; Violetta R. Beklemisheva; Alexander Graphodatsky; Shu-Jin Luo; Stephen J. O’Brien; Norman T.-L. Lim; Jason S. C. Chin; Vanessa Guerra; Gaik Tamazian; Arina Omer; David Weisz; Kenneth Kaemmerer; Ginger Sturgeon; Joseph Gaspard; Alicia Hahn; Mark McDonough; Isabel Garcia-Treviño; Jordan Gentry; Rob L. Coke; Jan E. Janecka; Ryan J. Harrigan; Jen Tinsman; Thomas B. Smith; Erez Lieberman Aiden; and Olga Dudchenko. 2023. "Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity." Chromosome Research , (13). doi:10.1007/s10577-023-09722-y.
DOI
10.1007/s10577-023-09722-y
Comments
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