Assembly updates

  • T.Hains & K.-P. Koepfli

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 flickr.com.
Manis javanica, photo by budak [CC BY-NC-ND 2.0], via flickr.com.

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 (https://www.dnazoo.org/assemblies/Phataginus_tricuspis), 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!

  • Ruqayya Khan

Native to the north African deserts, the fat-tailed gerbil, Pachyuromys duprasi, can be found after dusk scavenging for insects [1]. The fat-tailed gerbil is small and covered in long tan and gray fur with a white underbelly. Frequent sand baths keep their fur clean and healthy.

Like most desert dwellers, the fat-tailed gerbil has adapted to their dry environments. It survives by storing extra water and fats in their chubby tails, not unlike a camel’s hump [2]! One can gain insight into the health of fat-tailed gerbil by observing this plumpness of their stubby tails. A thin tail can indicate that the gerbil is lacking sufficient nutrients.

Fat-tailed gerbils by Peter Maas, [CC-BY-3.0], via eol.org

Their adaptation to conserve water may be why some rodent enthusiasts recommend keeping gerbils as pets over hamsters, as they typically use the bathroom less and aren’t as “stinky”. Additionally, the gerbil has a reputation of being calm and friendly towards humans. The fat-tailed gerbil is newer to the pet market compared to more commonly found Mongolian gerbil, but they are steadily gaining in popularity [3].

The gerbil community lovingly refers to this species of gerbils as “doops”, based off the pronunciation of their species name duprasi. These adorable animals can inspire a lot of joy in their owners. Check out for example these great illustrations by the artist PawLove of their doop, Pita!

Today, we share the genome assembly of the fat-tailed gerbil. Many thanks to Blossum from the Houston Zoo for providing the sample for this assembly! This is a $1K genome assembly with contig N50 = 48 Kb and scaffold N50 = 70 Mb (see Dudchenko et al., 2018 for procedure details).

If you’re interested in genome assemblies of some other great house pets, check out those for the golden hamster and the Chinese hamster on the DNA Zoo website!

With their round cheeks and happy smiles, Quokkas aka Setonix brachyurus have been dubbed the most cheerful animal on the planet. They eat flowers and carry their babies in pouches. They are adorable. No wonder the #QuokkaSelfie is going viral on Instagram and Twitter. Check those by @chrishemsworth @MargotRobbie and many more!

Setonix brachyurus, Quokka. Location: Australia, WA, Rottnest Island. Photo Credits: Microsoft Australia.

With the onset of Spring in September the adorable quokka joeys are ready to hop out from their mom’s pouches and into the big wide world. Time to have a birthday party!

After the inaugural Quokka Birthday in 2019, we are celebrating the 2nd Quokka Birthday today with the release of a chromosome-length genome assembly for these much-loved members of the kangaroo family.

Quokkas are listed as “vulnerable” by the IUCN and the Australian Department of Environment and Energy. The IUCN estimates that there are between 7,500 – 15,000 mature adults in the wild. The vast majority of these lives on Rottnest Island. There's also a protected population on Bald Island, and a few scattered colonies on mainland Australia.

The biggest threat to quokkas is deforestation. Humans are tearing down trees to build cities; weather changes are having ripple effects on vegetation, erosion, and rainfall. Wildfires are also a problem. E.g., in 2015, a wildfire in Western Australia decimated 90% of the local quokka population, with the estimated quokka numbers dropping from 500 to just 39. We hope that the new genome assembly will help monitor the population and inform the species management plans.

The genome assembly shared today was generated using two samples: one from Rottnest Island and one coming from a mainland quokka. This is a $1K genome assembly. See our Methods page for more details on the procedure!


Quokkas belong to the Macropodidae family of marsupials that includes kangaroos and wallabies. This is the 5th macropod in the DNA Zoo collection, after the tammar wallaby, Western grey kangaroo, Eastern grey kangaroo and red kangaroo. See below how the chromosomes in the new genome assembly relate to those of the tammar wallaby below! Looks like the genomes are highly syntenic, but 3 chromosomes in the tammar wallaby correspond to two distinct chromosomes in the quokka, chr #1 (chr #1+#10 in quokka), chr #3 (#5+#7 in quokka) and chr #6 (#6+#8 in quokka), explaining the difference in the karyotype.

Whole-genome alignment plot between the tammar wallaby chromosome-length genome assembly (me-1k, 2n=16) and the quokka genome assembly (Setonix_brachyurus_HiC, 2n=22). The chromosomes are largely syntenic with three chromosomes in tammar wallaby corresponding to two separate chromosomes each in the quokka.

If you are curious to know more about Rottnest Island Kingdom of the Quokka, please watch this Trailer from Sea Dog TV International on Vimeo. Better still, book a trip to Rottnest Island, Western Australia!


We gratefully acknowledge the collaboration and samples provided by Cassyanna Gray, Conservation Officer, Rottnest Island Authority, and Natasha Tay, Murdoch University. The work was supported by resources provided by DNA Zoo Australia, Faculty of Science, The University of Western Australia (UWA) and DNA Zoo, Aiden lab, Baylor College of Medicine (BCM). We are grateful for the computational support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. Additional computational resources and support was received via Microsoft AI for Earth grant.


The following people contributed to the project: Parwinder Kaur, Olga Dudchenko, David Weisz and Erez Aiden.

For more detail visit https://www.dnazoo.org/assemblies/Setonix_brachyurus.

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