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).

Victoria’s faunal emblem - fairy (Leadbeater's) possum

The Leadbeater's possum (Gymnobelideus leadbeateri) was named in 1867 after John Leadbeater, the then taxidermist at the Museum Victoria [1]. (They also go by the common name of fairy possum [2].) These cute little fairies which are just 33 cm (13 inches), tail included in body length, are rarely seen being nocturnal, fast-moving, and living in tree hollows of some of the tallest forest trees in the world [3]. They live in small family colonies of up to 12 individuals and mate twice per year, with a maximum of two joeys being born to each monogamous breeding pair in colony [4].

Leadbeater's possum (Gymnobelideus leadbeateri), image by Arabella Eyre, Zoos Victoria

The Leadbeater’s possums belongs to the Petauridae family together with the gliding possums. In contrast to other members of the family, Leadbeater’s possums do not glide, and are thought to represent an ancestral form that evolved about 20 million years ago [5].

The State of Victoria, Australia, made the Leadbeater's possum its faunal emblem on 2 March 1971 [6], and since then this emblematic species has almost gone extinct! It is now listed as critically endangered, largely restricted to small pockets of alpine ash, mountain ash, and snow gum forests in the Central Highlands of Victoria, Australia, north-east of Melbourne, with a single isolated population in lowland floodplain forest [7, 8, 9]. In the highlands, the February 2009 Black Saturday bushfires destroyed massive part of the reserve system of Leadbeater's possums' habitat, and the wild population is thought to have been drastically reduced in size.

The availability of suitable habitat is critical for saving the species from looming extinction. Intensive population recovery measures, including translocation, will be required to save the last lowland population. The loss of hollow-bearing trees is the possums' biggest threat in highland habitats, along with bushfire. Suitable hollows can take 190 years to develop in living trees, and old trees with suitable hollows have decreased due to logging and bushfires in the wild over the last three decades of the 20th century [10]. The animal’s vulnerability to fire makes climate change a severe danger.

To support ongoing conservation efforts led by Zoos Victoria, DNA Zoo has been working with Paul Sunnucks and Alexandra Pavlova at Monash University to get a chromosome-length assembly genome for a female belonging to the sole remaining population of fewer than 30 individuals of lowland Leadbeater’s possum, which experience harmful effects of inbreeding [11].

The chromosome-length assembly we share today is based on the draft assembly available on NCBI was generated by Han Ming Gan, Stella Loke and Yin Peng Lee of Deakin Genomics Centre, and the Monash University team, with funding from Zoos Victoria and Australian Research Council funded project LP160100482 (Gymnobelideus leadbeateri isolate B50252). The draft genome assembly was created using MaSuRCA v. 3.3.4 (Zimin et al. 2013), using Oxford Nanopore MinION reads polished with short-insert size Illumina NovaSeq reads.

The draft was scaffolded to 11 chromosomes with 250M Hi-C reads generated by DNA Zoo labs from a liver sample from the same isolate, obtained from Leanne Wicker and Dan Harley (Zoos Victoria), using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!

The Hi-C work was supported by resources provided by DNA Zoo Australia, Faculty of Science, The University of Western Australia (UWA), DNA Zoo, Zoos Victoria and Monash University, with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

See below how the chromosomes from the new Leadbeater's possum genome assembly related to those of another notable Australian mammal from our collection, the tammar wallaby. That's about 55MY of evolution separating the species [12]. Check out the assembly page for the $1K tammar wallaby genome assembly here!

Whole genome alignment plot between the Leadbeater's possum (LBP_v1_HiC) and the tammar wallaby (me-1k)

The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, David Weisz, Ruqayya Khan & Parwinder Kaur.

Blog by: Parwinder Kaur and Olga Dudchenko

Citations

Ruan, J. and Li, H. (2019) Fast and accurate long-read assembly with wtdbg2. Nat Methods doi:10.1038/s41592-019-0669-3

Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95. https://doi.org/10.1126/science.aal3327.

Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.

Durand, Shamim et al. “Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.” Cell Systems 3.1 (2016): 95–98.

James T. Robinson, Douglass Turner, Neva C. Durand, Helga Thorvaldsdóttir, Jill P. Mesirov, Erez Lieberman Aiden, Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data, Cell Systems, Volume 6, Issue 2, 2018