Announcements

  • Ruqayya Khan

The Risso’s dolphin, Grampus griseus, sets some impressive #travelgoals. Some estimates say that the Risso’s dolphin may spend as much as 77% of their lives traveling [1]! Their geographical range is spread across the world, although they prefer deeper waters over the coast. From temperate to tropical waters, the Risso’s dolphin can be found in pods of 10-30 individuals [2].


Sometimes called the gray dolphin, the coloring of this species changes with age. Risso’s dolphins start their lives as black or dark gray in color and then lighten to a gray/white as they mature. The skin of this species is often marked by many scars, usually caused by teeth raking from other dolphins [3].


Unlike most cetaceans, the Risso’s dolphin lacks any upper teeth but instead can have several rows of peg-like teeth on their lower jaw. These teeth are useful in catching their preferred prey the cephalopods and also may play a role in mating behavior [4].

Risso's Dolphin, Grampus griseus by Robin Agarwal, [CC BY-NC 2.0], via flickr.com.

Today, we share the chromosome-length assembly for the Risso’s dolphin. This is a $1K de novo genome assembly with a contig N50 = 62 Kb and a scaffold N50 = 93 Mb. See Dudchenko et al., 2018 for details on the assembly procedure.


The sample for this genome assembly was provided to us by Barbie Halaska, Necropsy Manager at The Marine Mammal Center in Sausalito, California. As the world’s largest marine mammal hospital, the Center prides itself on gathering and providing open research data that is free to access, reuse, repurpose and redistribute in service to ocean conservation and marine mammal health.


This sample was collected by The Marine Mammal Center under the Marine Mammal Health and Stranding Program (MMHSPR) Permit No. 18786-04 issued by the National Marine Fisheries Service (NMFS) in accordance with the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The work at DNA Zoo was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03.


Want to compare this genome against other members of the Delphinidae family? You’re in luck as this is the DNAZoo’s 8th genome assembly of a dolphin species! Check out the assembly pages for the bottlenose dolphin and the Commerson’s dolphin.


We thank Barbie Halaska, Laura Sherr, Giancarlo Rulli and Ben Neely for their help with this genome assembly!


Learn more about the impact of The Marine Mammal Center’s scientific research by visiting the TMMC website at MarineMammalCenter.org.


  • 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!

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