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

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作   者：

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-Trevino, Isabel;  Gentry, Jordan;  Coke, Rob L.;  Janecka, Jan E.;  Harrigan, Ryan J.;  Tinsman, Jen;  Smith, Thomas B.;  Aiden, Erez Lieberman;  Dudchenko, Olga; 

作者机构：

RAS;  Univ Calif Los Angeles;  Simon Fraser Univ;  Ctr Computat Biol;  Conservat Sci & Wildlife Hlth;  Univ Chicago;  Dept Biol Sci;  Ctr Conservat & Res;  Globe Inst;  Peking Univ;  Ctr Genome Architecture;  San Diego Zoo Wildlife Alliance;  Pittsburgh Zoo & Aquarium;  Bayer Sch Nat & Environm Sci;  Peking Tsinghua Ctr Life Sci CLS;  Univ Copenhagen;  Dept Divers & Evolut Genomes;  Baylor Coll Med;  ITMO Univ;  Inst Environm & Sustainabil;  Duquesne Univ;  Lab Genom Divers;  Natl Inst Educ;  Peter Great St Petersburg Polytech Univ;  ITMO University;  Nanyang Technol Univ;  Comm Evolutionary Biol;  Taipei Zoo;  San Antonio Zoo; 

关键词：

chromosome number;  SYSTEM;  NUMBER;  REARRANGEMENTS;  genome assembly;  PRINCIPLES;  karyotype;  EVOLUTION;  ALIGNMENT;  MAPS;  Phataginus tricuspis;  KARYOTYPE;  PROVIDES;  Pholidota; 

期刊名称：

Chromosome research: An international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

i s s n：

0967-3849

年卷期：

2023 年 31 卷 2 期

页   码：

Article: 13-Article: 13

页   码：

摘   要：

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.