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

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).