Happy Birthday to Happy Quokka!

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.

Messin' with Mesoplodonts

Today, we release the genomes of three Mesoplodont whales: the Blainville's beaked whale Mesoplodon densirostris, the Gervais' beaked whale Mesoplodon europaeus, and the Stejneger's beaked whale Mesoplodon stejnegeri.

The three Mesoplodont whales from today's release: the Blainville's beaked whale (top), Gervais' beaked whale (bottom left) and Stejneger's beaked whale (bottom right). Credit: NOAA Fisheries.

These three species of Mesoplodon are beaked whales in the Ziphiidae family. Interestingly, all three have interesting nicknames: Blainville’s are referred to as the “dense-beaked whale”, Gervais’ are referred to as the “Gulf Stream beaked whale” and Stejneger’s are referred to as the “saber-toothed whale”. There are more than 20 species of Ziphiidae, but the vast majority of known species are Mesoplodonts (15 species). The beaked whale family has relatively small body sizes (roughly 15 to 20 feet long and 2000 to 3000 lbs), as well as elusive and shy behavior around humans, and inconspicuous blow. They are also difficult to identify in the wild since they mostly lack easily discernible physical characteristics. These traits make them difficult to study, to say the least. Although beaked whales comprise roughly a quarter of recognized cetacean species, information on their behavior and population numbers is largely unknown. For instance, a live Gervais’ beaked whale wasn’t seen in the wild until 1998 (though here is some video of one swimming).

Although we know very little of these elusive cetaceans, we do know they are deep divers. Beaked whales eat deep-sea and open-ocean species of fish (e.g., mackerel, sardines, and saury), as well as crustaceans, sea cucumbers, squid, and octopus. They use echolocation on their deep dives to find prey, and once located they suction them into their mouth. These three beaked whales inhabit deep waters (600 to 5000 ft) around the northern hemisphere. The Stejneger's beaked whale prefers the cold water of the North Pacific Ocean is the only Mesolplodont in Alaskan waters, while the Blaineville’s beaked whale lives in tropical to temperate waters worldwide including the Pacific and Atlantic Oceans and the Gulf of Mexico. (The specific animal assembled today is of the Western North Atlantic stock.) The Gervais’ beaked whale prefers deep warmer seas of the Atlantic Ocean, but can be found occasionally in colder waters. (The specific animal assembled here is from the Western North Atlantic stock.)

We are also working on hard on other cetaceans, including more beaked whales like the Cuvier's beaked whale Ziphius cavirostris, so stay tuned as we have a whale of time!

All genomes were generated following the $1K strategy described in (Dudchenko et al., 2018). See our Methods page for more details.

This work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The Blainville's beaked whale (Mesoplodon densirostris) specimen used in this study was collected by NOAA (Wayne McFee) from Sullivan's Island, SC. The Gervais' beaked whale (Mesoplodon europaeus) specimen used in this study was collected by NOAA (Wayne McFee) from Georgetown, SC. The Stejneger's beaked whale (Mesoplodon stejnegeri) specimen used in this study was collected by Alaska Sealife Center (Pam Tuomi) from Whittier, AK. The specimens were provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program and the Alaska Marine Mammal Tissue Archival Project.

Hawaiian monk seal

Unlike most pinnipeds, monk seals are found in temperate subtropical oceans. There are currently two species in two genera, Neomonachus schauinslandi in the Hawaiian archipelago and Monachus monachus in the Mediterranean. Until it became extinct by the 1950s, a third species Neomonachus tropicalis was found in the Caribbean and evidence suggests that they and their Hawaiian cousins diverged with the closing of the Isthmus of Panama.

Today, monk seals are endangered and the Hawaiian seal has been the subject of a NOAA led recovery effort. As a consequence of that program and the efforts of volunteer and non-profit conservation groups (see monksealmania.blogspot.com and www.marinemammalcenter.org/) the species is slowly recovering. Together, these groups monitor animals, tag pups and provide veterinary care to animals that are injured or in need of medical intervention.

“Benny” the Hawaiian monk seal enjoying a long, undisturbed nap on a beach on Oahu. Photo by Alan Scott.

We sequenced a particular Hawaiian monk seal named “Benny” who lives largely in the waters around Oahu. I was introduced to Benny on a nature tour of the island in 2009 and was amused that he had been cordoned off with stakes and tape that looked a bit like a crime scene. Benny was sound asleep and oblivious to tourists taking pictures of him. I happened to be back in the same area the next day and stopped out of curiosity to see if he was still there. Not only was he there but in exactly the same location and looked like he had not moved a muscle. This led me to follow his exploits and over the years I learned that he was the subject of a coloring book about keeping the beaches clean and had been captured at least twice for emergency medical procedures after swallowing fish hooks. The latter was an opportunity to get blood samples shipped to Baltimore where we isolated DNA and over the past several years have used it to test various methods of genome assembly including linked-read sequencing (https://www.biorxiv.org/content/10.1101/128348v2.full.pdf).

Recently, we joined the linked-read sequencing assembly with some Hi-C data to generate the chromosome-length genome assembly, now available on DNA Zoo website and soon to appear on NCBI.

We expect that Benny’s sequence will help with conservation efforts (e.g., he has a very low level of heterogeneity across his genome and in his MHC loci that may make him susceptible to disease) as well as let us better understand the evolutionary relationships between seals and other carnivores.

The Hawaiian monk seal genome assembly is the 4th Phocidae (earless seal) genome assembly on the DNA Zoo website, after the Northern elephant seal, the bearded seal and the harbor seal. Check out below the whole-genome alignments between the 4 species. The earless seals appear to have a highly conserved karyotype, with 1 fusion apparent in the harbor seal as compared to the other 3 seal species.

Whole-genome alignment plots between the new genome assembly for the Hawaiian monk seal (Neomonachus_schauinslandi_HiC) and those for the bearded seal, the harbor seal and the Northern elephant seal (Erignathus_barbatus_HiC, GSC_HSeal_1.0_HiC and Mirounga_angustirostris_HiC).