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).

Another milestone reached

We are happy to report that last week we passed the milestone of 150 shared genome assemblies on our website. Our assembly page features chromosome-length fastas and Hi-C contact maps for 133 vertebrates (including 117 mammals), 9 plants, 6 insects, 2 mollusks and 1 flatworm.

To commemorate, we do another round of data submission to NCBI Sequence Read Archive, shared under the DNA Zoo BioProject accession PRJNA512907.

Some statistics for the data available:

· 181 biosamples,

· 284 Hi-C experiments across 156 species,

· 44 DNA-Seq experiments across 44 species,

· total number of bases: 20,061,496,464,054!

We thank Illumina, Macrogen, Novogen, the Broad Institute and Baylor College of Medicine GARP core and Baylor Genetics for their help with the data production!

As before, we share the data without restrictions: see our data usage policy here.

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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