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Many scales, many chromosomes!

Klaus-Peter Koepfli, Marlys Houck, Erez Aiden, and Olga Dudchenko

Pangolins, also known as scaly anteaters, belong to an entirely distinct order of mammals known as the Pholidota (from Greek meaning “horny scale”). DNA evidence has established that the closest living group to the pangolins is the Carnivora, the order containing the cats, civets, mongooses and hyenas as well as the dogs, bears, raccoons, weasels, seals and sea lions. The earliest pangolin fossils date from the Eocene (~34 to 56 million years ago), but molecular dating suggests the ancestors of Pholidota may originated around 80 million years ago in the Cretaceous.

The 8 living species of pangolins were originally classified in the genus Manis, but analyses based on fossils, morphology, and molecular data indicate that the species are divided into three well defined genera: Manis (Asian pangolins, 4 species), Phataginus (African tree pangolins, 2 species) and Smutsia (African ground pangolins, 2 species).

Pangolins are among the most unusual of mammals when it comes to their biology. Along with their bodies being covered in sharp, keratinized scales which provides armor against predators when they roll up into a ball, pangolins lack teeth and instead use their extremely long tongue and sticky saliva to feed on ants and termites. Interestingly, molecular genetic and genome studies have shown that several genes involved in the development of teeth have become pseudogenized in pangolins. They possess long and thick claws at the ends of their powerful limbs which they use to dig burrows, break open ant and termite nests and to climb trees.

Pangolins are considered the most illegally trafficked mammals in the world. They are heavily poached due to the high demand for their scales, which are used in Asian traditional medicines, and for their meat. The eight species are listed as either Threatened or Critically Endangered on the IUCN Red List of Threatened Species. Vigorous international efforts are trying to curtail the illegal trafficking of pangolins in order to prevent their extinction. You can learn more about pangolins and their conservation on the Save Pangolins website.

Pangolins have also been in the news recently because of their possible link to the novel coronavirus that has been infecting people within and outside of China. Several studies have reported evidence that the Malayan pangolin (Manis javanica) to be a possible intermediate host and reservoir of coronaviruses that are related to the novel human coronavirus causing COVID-19 [1, 2, 3]. However, these studies have not been formally peer-reviewed and therefore, the conclusions should be interpreted with caution.

Today, we are proud to share the very first chromosome-length assembly of one of the 8 species of the Pholidota, the white-bellied or tree pangolin (Phataginus tricupis) from Africa. The assembly was generated from a female white-bellied pangolin named “Jaziri” who is housed at the Pittsburgh Zoo & PPG Aquarium, in Pittsburgh, Pennsylvania. The chromosome-length assembly is based on a draft assembly generated using 10x Genomics linked-read sequencing and Supernova version 2.0.1.

Jaziri’s assembly revealed an amazing finding: the presence of as many as 114 diploid chromosomes! This discovery was first observed independently in 2009 in standard giemsa stained and C- and G- banded karyotypes from several individuals of white-bellied pangolin from San Diego Zoo’s Frozen Zoo®. This was unexpected because previous karyotype studies of three Asian pangolin species (Chinese, Indian and Malayan) showed a chromosome complement between 2n=36-42. This would also make white-bellied pangolins the mammal species outside of the Rodentia (mice, rats, squirrels and their allies) with the highest number of chromosomes, among those whose karyotype has been examined. The current record holder for highest chromosome number in mammals is the Bolivian bamboo rat, Dactylomys boliviensis, with a 2n = 118, which in 2001 broke the record of 2n=102, previously held by another rodent, the red vizcacha rat, Tympanoctomys barrerae, which was reported in 1990 [4]. The karyotypes of the San Diego animals show the presence of many small chromosomes and Jaziri’s Hi-C contact map show the presence of many small c-scaffolds, which likely correspond to these very small physical chromosomes. A manuscript describing these results is in preparation.

Jaziri’s assembly was made possible through a collaboration of the following individuals: Tom Smith, Department of Ecology and Evolutionary Biology and Director of the Center for Tropical Research at UCLA; Klaus-Peter Koepfli, Center for Species Survival, Smithsonian Conservation Biology Institute; Kenneth Kaemmerer, Curator of Mammals, and Ginger Sturgeon, Director of Animal Health, Pittsburgh Zoo & PPG Aquarium; Jan Janecka, Department of Biological Sciences, Duquesne University; and Olga Dudchenko, Arina Omer and Erez Aiden, The Center for Genome Architecture, Baylor College of Medicine and Rice University. Karyotypes of the San Diego Zoo pangolins were made possible by Marlys Houck, Julie Fronczek and Ann Misuraca, San Diego Zoo Institute for Conservation Research.

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