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Scaling up genomes of scaly pangolins

Pangolins are some of the most interesting animals on the planet both from the perspective of biology as well as pangolins being the most illegally trafficked mammal in the world. Pangolins are the sole members of the mammalian order Pholidota (which is Greek for “horny scale”), which is split into three genera: the Asian pangolins (genus Manis), the African tree pangolins (genus Phataginus), and the African ground pangolins (genus Smutsia).

Due to the illegal wildlife trade for pangolin scales, which are highly valued in the Asian traditional medicine markets, populations of pangolin species in both Africa and Asia are rapidly decreasing. The Asian species are typically smaller than their African counterparts, with tens of thousands of animals trafficked illegally each year. The eight known pangolin species are listed as either Vulnerable, Endangered, or Critically Endangered according the IUCN Red List of Threatened Species. Many international efforts on both policy and scientific fronts are aiming to prevent the extinction of these species and you can learn more about pangolin conservation efforts by visiting the Save Pangolins website.

Time-calibrated, molecular phylogenetic tree of pangolins, summarizing their distribution and revised classification. Time to most recent common ancestors (in million years) are indicated at the tree nodes. From Gaubert et al. (2017).

Recently, we released a chromosome-length assembly for the African tree pangolin, here. Today, we follow-up with chromosome-length assemblies for two Asian species of pangolins: the Malayan pangolin (Manis javanica) and the Chinese pangolin (Manis pentadactyla). These genome assemblies are upgrades from the drafts published by (Choo, Rayko et al., 2016).

Manis pentadactyla. Photo credit to Ms. Sarita Jnawali of NTNC – Central Zoo [CC BY 2.0], via
Manis javanica, photo by budak [CC BY-NC-ND 2.0], via

The Chinese pangolin can be found in northern India and Southeast Asia as well as southern China, while the Malayan pangolin can be found throughout Southeast Asia.

In contrast to the previously reported tree pangolin (Phataginus tricuspis) genome assembly (, which possess 57 (!) chromosome pairs making the tree pangolin the mammal with one of the largest chromosome count out there, the Malayan pangolin possesses only 19 chromosome pairs while the Chinese pangolin possess 20 chromosome pairs. See how the chromosomes of the three species relate to each other in the whole-genome alignment plot below.

Whole-genome alignments between the new chromosome-length genome assemblies of the the Malayan (ManJav1.0_HiC), the Chinese (M_pentadactyla-1.1.1_HiC) pangolin and the tree pangolin (Jaziri_pseudohap2_scaffolds_HiC).

According to Gaubert et al. 2018, the genus Manis split from the African genera roughly 38 million years ago and the split between the Malayan and Chinese pangolin is estimated at about 13 million years ago. This makes Pholidota a remarkable group in studying genome rearrangements and the role of chromosome numbers in diversification and speciation.

Lastly, pangolins are susceptible to coronaviruses, and there have been many mentions of pangolins in the media in relation to COVID-19 as a possible intermediate host for the transmission of SARS-CoV-2 to humans. The data does not seem to link pangolins directly to the current outbreak, but a virus related to pangolin coronavirus may have donated a receptor-binding domain to SARS-CoV-2 (Xiao et al., 2020). More generally, pangolin coronaviruses could represent a future threat to public health if wildlife trade is not effectively controlled.

If you happen to have samples for the African ground pangolins, please reach out. We’d love to work together to fill in the gaps in the pangolin phylogeny!

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