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

Don't worry be capy!

The capybara is the largest living rodent in the world! Their scientific name, Hydrochoerus hydrochaeris, comes from the Greek words “hydor” meaning water and “choiros” meaning pig. Native to South America, these oversized rodents are well adapted to life on land and in water. Capybaras can be found inhabiting flooded grasslands, swamps, as well as the banks of rivers and lakes. One can say capybaras were made to swim with their webbed feet and their wiry, quick-drying hair that’s perfectly suited for moving land and water frequently [1].

Image by Karsten Paulick from Pixabay [Pixabay License], via pixabay.com

Capybaras are very social animals, living in groups ranging from 3 to 30 individuals [2]! They are very communicative, producing various types vocalizations. Similar to beavers, the front teeth of the capybara never stop growing [3]. Capybaras must continually gnaw and chew on grasses and aquatic vegetation to keep their teeth size in check. Just like their close relatives, the guinea pigs, capybaras must eat their feces to get beneficial bacteria to help their stomach break down the fiber in their meals.

Today we share the chromosome-length assembly for the capybara. This is a $1K genome assembly with a contig n50 of 79 Kb and a scaffold n50 of 71 Mb. Check out Dudchenko et al., 2018 for procedure details. Thank you to Pop from the Houston Zoo for providing us with the sample to make this assembly possible! See Pop bonding with his keeper here!

Capybaras are legal to own as pets in some states in the US, and owning a capybara is a relatively recent trend in the pet world. This has already had some consequences: did you know that the state of Florida is dealing with a problem of invasive capybaras, most likely due to them escaping or being released by irresponsible owners?

Some may say that the capybara is basically an oversized guinea pig, but the genomics says otherwise. Just look at the many rearrangements between the two species! Check out our assembly page for the domestic guinea pig here.

Whole genome alignment plot for the capybara against the domestic guinea pig (Cavpor3.0_HiC).