Quollity genomic resource

The Northern quoll (Dasyurus hallucatus) is the smallest of the four Australian quoll species with adults weighing around 0.5-1 kg (males are larger than females). Northern quoll populations have declined by more than 75% since the introduction of poisonous cane toads, which the quolls mistake for food.

Photo Description: Northern Quoll (Dasyurus hallucatus). Photo credits: S J Bennett, CC BY-NC 2.0, via Creative Commons

The Northern quoll is a medium-sized carnivorous marsupial found in northern Australia. Northern quolls are relatively short-lived for an animal of their size, especially males which in the wild normally die soon after mating at only 1 year of age before their own offspring are born. During the mating season (around June to September), males expend considerable energy fighting other males, and do not survive to breed a second year. Females den in tree hollows, hollow logs and rock crevices; they raise a litter of up to eight young. At the end of the breeding season, the Northern quoll population is comprised almost entirely of mature females and their young. Females may live for two or three years.

Once widespread across northern Australia, the northern quoll now only occurs in fragmented populations and is classified as endangered by the IUCN. They reported to be critically endangered in the Northern Territory, and populations in Western Australia are vulnerable to extinction at very fast rates. The northern quoll's demise is attributed to several factors, including predation by invasive pests and habitat destruction, but more notably its predation on the toxic introduced cane toad. Several strategies are currently being investigated to combat the threat of cane toads, including targeted gene flow, training aversion behaviour, and engineering genetic resistance to the toad's toxin.

To support the above conservation efforts further, we share the first chromosome-length genome assembly for the northern quoll. This is a collaborative effort of DNA Zoo labs with Assoc. Prof. Ben Phillips and Dr Stephen Frankenberg from University of Melbourne along with Dr Adnan Moussalli from Museums Victoria. The chromosome-length assembly is based on a draft assembly produced using 10x Genomics Chromium linked-read sequencing of a male northern quoll fibroblast cell line, established from a tissue sample kindly provided by the Territory Wildlife Park, and assembled using Supernova with additional funding from the Hermon-Slade Foundation.

A liver sample from the same animal was used for the Hi-C sequencing. The 10X draft assembly was scaffolded with 722,045,107 PE Hi-C reads generated by DNA Zoo labs and processed using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details. Check out the interactive contact map of the Northern quoll’s 7 chromosome-length scaffolds below!

We hope that this assembly will provide a valuable genomics resource for northern quoll conservation, including the analysis of population genetics data and the development of genetic strategies to enable population recovery.

We gratefully acknowledge the resources provided by The University of Melbourne, Museums Victoria, The University of Western Australia and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre.

Keeping it batty

One of the largest bat species in the world, the Indian flying fox (Pteropus medius aka Pteropus giganteus) can have wingspans of 1.2 - 1.4 meters wide [1]! Though they can look intimidating in flight, have no fear! For the Indian flying fox primarily eats fruits and nectar. In fact, they are often viewed as pests by farmers due to the destruction they can wreck on farms and orchards. That being said, the Indian flying fox plays an integral role in pollination and seed dispersal of many keystone plants in their home range across the Indian subcontinent [2].

Indian Flying Fox by Sergey Yeliseev, [CC BY-NC-ND 2.0], via flickr.com

The Indian flying fox can live in large roosts, sometimes comprising of hundreds of individuals! These roosts can be occupied for over a decade, preferring to roost in trees such as the banyan, fig, and tamarind trees. These large roosts are ideal for the Indian flying fox, as they are polygynandrous, or where both male and female bats mate with multiple partners in a breeding season [3].

As zoonotic diseases become more of concern, virologists and epidemiologists have been particularly interested in the Indian flying fox, a known asymptomatic carrier for the Nipah virus. Humans infected with the Nipah virus can experience encephalitis, severe illness, and death. Understanding the unique features of the Indian flying fox genome may help researchers identify evolutionary features of zoonotic diseases, like the Nipah virus.

Pteropus giganteus colony, Goa, India by Vladimir Yu, Arkhipov, Arkhivov, [CC BY-SA 3.0], via wikimedia.org

Today, we share the chromosome-length assembly for the Indian flying fox, Pteropus giganteus also known as Pteropus medius (read more about the naming issue on Wikipedia). This genome is a Hi-C upgrade for the draft genome assembly generated by Fouret et al., (2020). Many thanks to the Houston Zoo for providing the sample used for this chromosome-length Hi-C upgrade. Please visit our Methods page for more details on the assembly procedure, and check out the interactive Juicebox.js map below for the Hi-C contact map of the 19 chromosomes of the Indian flying fox!

This is our 11th bat species released here on the DNA Zoo blog and the third Pteropus bat, or mega-bats genus! While you're here, don't forget to check our the assembly pages for the large flying fox (Pteropus vampyrus) and the Madagascan flying fox (Pteropus rufus). Stay tuned for more bat genomes to come, and Happy Bat Week!

Citations: Fouret, J., Brunet, F.G., Binet, M., Aurine, N., Enchéry, F., Croze, S., Guinier, M., Goumaidi, A., Preininger, D., Volff, J.-N., Bailly-Bechet, M., Lachuer, J., Horvat, B., Legras-Lachuer, C., 2020. Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding. Front. Microbiol. 11, 1807. https://doi.org/10.3389/fmicb.2020.01807

Living gold of snowy Siberia

The sable, Martes zibellina, is an active and agile predator slightly smaller than a house cat. It has excellent hearing and vision thanks to its big ears and eyes, and a keen sense of smell. With its flexible body and long strong legs, the sable feels equally comfortable on the ground, under the snow, and high up in tree crowns. Its color is quite variable – from pale greyish-buff to rich brown to jet black, usually with a paler face, darker dorsal stripe, tail and paws, and a contrasting irregular-shaped throat patch, which is sometimes small or absent; some individuals have white guard hairs uniformly “sprinkled” all over their bodies. Most of its range lies in Siberia, from the Ural mountains to the Kamchatka peninsula; there are some sables in northeastern Kazakhstan, in Mongolia and northeastern China, and on a number of islands off the Pacific coast of Eurasia, including Sakhalin, some of the Kurils, and the island of Hokkaido.

Sable marten by Е.Медведева, [CC BY-SA 3.0], via Wikimedia Commons

Like other martens, the sable gravitates towards large contiguous areas of old-stand, mainly coniferous forests with lots of dead wood to provide shelter, nesting and a good supply of small rodents, including its main target – the red-backed vole (Clethrinomys spp.). However, it can take down prey several times its size and weight, such as capercaillies, mountain hares, and small ungulates such as the Siberian musk deer or even roe deer trapped in deep snow. It will use any calories it can find: in years with a good crop of Siberian pine cones, it will feed almost exclusively on pine seeds, and in some years, it will venture out into peatbogs and eat cranberries until the snow becomes too deep. It thrives in a variety of habitats and climates, be it the forest-tundras of the Yamal peninsula, bogged coniferous taiga of Yugra, birch-covered forest-steppes of Southwest Siberia, larch hills of Yakutia, or coastal rainforests of northern Japan. Still, the sable is a quintessential cold-climate animal and is extremely well-adapted to life in deep snow: by late October, it grows a thick, soft winter coat that protects it from extreme temperatures, and long bristles on its well-furred feet that allow it to cover long distances in deep fluffy snow, looking for food; thick snow cover provides shelter from the elements, and during cold spells, when temperatures drop below -40 F, sables are known to spend up to two weeks in the snow without surfacing. How they do it is a bit of a mystery, as they have fast metabolism, do not have any significant fat deposits, and cannot hibernate.

Figure 1. USSR natural taxes on fur in 1921 (in Russian). 1 dark sable pelt = 4 polar bear pelts = 15 snow leopard pelts = 1000 squirrel pelts = 18000 ground squirrel pelts

In the western part of its range, east of the Urals and across the West Siberian plain, the sable occurs together with the closely related pine marten (Martes martes), a similarly sized, more uniformly-colored mustelid with coarser fur and longer, fuzzier tail, which is believed to be adapted to slightly warmer climates and more arboreal lifestyle; the two species often produce apparently fertile hybrids; such a hybrid is called a kidus, or kidas, in Russian, and usually has mixed morphological features from both parents.

The crave for the silky-furred mustelid was the driving force behind the conquest of Siberia by the Russian Empire; sable pelts were a royal luxury, commanding sky-high prices, and remained a key export of the state well into the Soviet times. This illustration shows a natural tax imposed upon hunters by the Bolshevik government: a single sable skin equaled three snow leopards or 1000 squirrels! Even nowadays, harvested sustainably, sable fur remains a major source of sustenance for thousands of people in Siberia, especially in areas such as Evenkia and Yakutia, where the climate is too harsh and unpredictable for dependable agriculture.

Early in the XX century, a catastrophic decline of the species occurred throughout its range, caused by hunting pressure and quite possibly other factors, because simultaneously, a similar decline happened with the North American marten even in areas where trapping pressure was insignificant. In 1935-1940, the Soviet government imposed a total ban on sable hunting and trapping and launched a massive reintroduction program. Hundreds of sables were live-trapped, primarily East of Baikal, in Yakutia and on Kamchatka, where the darkest and thus the most valuable forms of the sable occur, transported over thousands of miles by air, by train, and even on reindeer sleds, and released in various locations all over Siberia. This worked, and within a decade, the numbers of the species rebounded back to healthy levels. Unfortunately, the wildlife management science of the time had little concern for the well-being of infraspecific taxa, and some subspecies of the sable were probably lost or dissolved in the progeny of those introduced individuals. We are yet to understand the impact of the reintroduction program on the morphological and genetic diversity of the sable – a challenge where this study will come in so handy!

Today, we present the chromosome level assembly for the sable marten, Martes zibellina. This is the fourth species in the genus Martes we have released here on the DNA Zoo. All C-scaffolds of the sable were assigned to the corresponding chromosomes via a Zoo-FISH experiment with the stone marten chromosomes used as probes. Both the sable and stone marten have the same diploid number of chromosomes (2n=38) with no detected translocations, so we arranged the sable chromosomes in the same order as in the stone marten karyotype. Among other types of rearrangements several inversions were observed (Fig. 2).

Figure 2. Dotplot for whole genome alignment of sable genome to stone marten assembly

Check out the interactive Juicebox.js session below for a Hi-C contact map of the 19 sable chromosomes, and don't forget to visit the assembly page for more details about the assembly procedure!

This work was performed with funding from Dr. Rogell Powell (North Carolina State University) for 10x Genomics linked-read sequencing for the draft assembly. Dr. Klaus Koepfli (Smithsonian-Mason School of Conservation) and Dr. Alexander Graphodatsky (Institute of Molecular and Cellular Biology, Russia; IMCB) organized and brought all of the collaborators together to achieve chromosome-length genome assembly for the sable. Samples from a female M. zibellina were provided by Tatiana Bulyonkova. The fibroblast cell line was established by Dr. Polina Perelman (IMCB). Cultured cells (passage 3) were used for both DNA extraction for linked read sequencing and for Hi-C experiments (passage 9). High-molecular weight DNA was extracted by Natalia Serdyukova (IMCB). Zoo-FISH experiments were performed by Dr. Violetta Beklemisheva (IMCB). The initial assembly was performed by Sergei Kliver (IMCB). Hi-C experiments and scaffolding to chromosomes were done by Ruqayya Khan, David Weisz and Olga Dudchenko. The genome annotation and a paper describing this research is in progress. IMCB work was supported by RFBR grant № 20-04-00808 and grants to A.S. Graphodatsky: RSF 19-14-00034 and Program of fundamental research of state academies of sciences 0246-2021-0015.

There is a massive body of studies on sable ecology, physiology and genetics conducted by many prominent Russian scientists: D.V. Ternovsky (“Biology of mustelids”, 1977), Yu.G. Ternovskaya, A. S. Graphodatsky (Novosibirsk), G.I. Monahov, V.G. Monahov (Ekaterinburg), A.V. Abramov (St. Petersburg), V.V. Rozhnov (Moscow), K.G. Abramov (St. Petersburg), P.B. Yurgenson (Moscow), S.I. Ognev (Moscow) and many others. Sable has 2n=38 with relatively small amount of heterochromatin compared to other mustelids (Graphodatsky et al., 1976, 1977, 2020; Orlov, Malygin, 1969).

And finally, if you're interested in more marten genomes, please check out the assembly pages for the pine marten, stone marten, and the yellow-throated marten. This is the 5th species lead by the DNA Novosibirsk team, be on the look out for many more to come!

Citations:

1. Atlas of mammalian chromosomes (2nd edition). eds. Graphodatsky AS, Perelman PL, O’Brien SJ. Wiley-Blackwell, USA, 2020, 1008 p.

2. Graphodatsky A.S., Volobuev V.T., Ternovsky D.V., Radjabli S.I., 1976. G-staining of chromosomes of seven mustelidae species (Carnivora, Mustelidae). "Zool. J.", 55: 1704-1711.

3. Graphodatsky A.S., Ternovskaia Ju.G., Ternovsky D.V., Radjabli S.I., 1977. G- and C-bands and amount of DNA in sable. "Tsitol. Genet.", 11: 483-485. (Rus.)

4. Graphodatsky A.S., Radjabli S.I., 1988. Chromosomes of rural and laboratory mammals. Atlas. “Nauka”, Novosibirsk. (Rus.)

5. Orlov V.N., Malygin B.M., 1969. In: Mammals, N.N.Vorontsov, Ed., Novosibirsk. (Rus).

6. Ternovsky D.V. Biology of mustelids. Ed. Maksimov A.A., Nauka (Novosibirsk), 1977, 280 pp.