Eastern water dragon

The Eastern Water Dragon (Intellagama lesueurii) is one of Australia's largest dragon lizards and can be found living in both natural waterways and within highly developed city centres. Previously Physignathus, Intellagama has only recently been considered its own distinct genus translating to "smart dragon". The specific name lesueurii honours the French naturalist Charles-Alexandre Lesueur (1778-1846) who collected this species on the Baudin expedition of 1800.

Photo Description – The Eastern Water Dragon (Intellagama lesueurii). Photo credits: Celine Frere, University of the Sunshine Coast [CC].

Water Dragons are found in eastern Australia, where there are two subspecies. The Eastern subspecies (Intellagama lesueurii lesueurii), occurs along the east coast of Australia from Cooktown in the north down to the New South Wales south coast (approximately at Kangaroo Valley) where it is replaced with the Gippsland subspecies (Intellagama lesueurii howittii), which is distributed as far south and into the Gippsland region of eastern Victoria.

Water Dragons are a charismatic species that can live in large social groups often communicating through a variety of dominant and submissive signals including head-bobbing, arm waving and push-ups. The Water Dragon is a familiar sight in Australian cities and urban areas, where they have become habituated in parks and botanical gardens. Several inner-city populations narrowly separated by urban landscape have begun to diverge from one another, becoming genetically and morphologically distinct. These city slicker dragons have demonstrated that under some circumstance’s evolution can proceed at a significantly faster pace that initially thought.

Although not listed as threatened, Water Dragons are protected in all states and territories where they occur naturally: Queensland, New South Wales, Australian Capital Territory and Victoria.

Today, we share the chromosome-length assembly for the Eastern Water Dragon. DNA Zoo has been working with Associate Prof Celine Frere, Dr Dan Powell and Nicola Kent at The University of Sunshine Coast, Australia to deliver this much required key fundamental genomic resource.

The assembly is based on a draft hybrid assembly effort supported by The Australian Amphibian and Reptile Genomics Initiative (AusARG), a collaborative at Bioplatforms Australia framework initiative building genomic resources for thorough understanding of evolution and conservation of Australia’s unique native Amphibians and Reptiles that are now under threat, through climate, disease or habitat modification. The draft genome assembly was created using high-fidelity long reads from Pacific Biosciences technology (circular consensus sequencing). The reads were assembled using the long-read assembler Hifiasm (Cheng et al., 2021).

The above draft was scaffolded with 118,960,506 PE Hi-C reads generated by DNA Zoo labs 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, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

The new genomic tools and resources for the Eastern Water Dragon (Intellagama lesueurii) will enable detailed investigations into their unique ability to adapt to life in our highly urbanised cities and facilitate a better understanding of how reptiles can respond to rapid environmental change.

The following people contributed to the Hi-C chromosome-length upgrade of the draft assembly: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.

Blog by: Parwinder Kaur, Nicola Kent, Dan Powell and Celine Frere.

Citations:

Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021). https://doi.org/10.1038/s41592-020-01056-5

Hungry worm seeks sheep

Teladorsagia circumcincta aka brown stomach worm is a nematode that is one of the most important helminth parasites causing gastroenteritis in sheep and goats worldwide. It infects the fourth part of the compound stomach (abomasum) of these ruminants and elicits a type 2 immunity that can lead to host inflammatory immune responses associated with mucosal damage and protein-losing gastropathy.

Photo Description – A montage image of Teladorsagia circumcincta female with prominent vulval flap at the posterior end with a scale of 1mm and the background has been digitally altered to be consistently black. The sample is unaltered.Photo credits: A/Prof. Peta L. Clode, Centre for Microscopy, Characterisation and Analysis, UWA

The brown stomach worm is common in cool, temperate areas, such as south-eastern and south-western Australia and the United Kingdom. The infection occurs through feacal-oral route and leads to disruption in gastric mucosa, oedema of abomasal folds, and sloughing of mucosaethat can result in increased mucus production, decreases in acid production, increased serum pepsinogen levels and protein deficiency (hypoalbuminemia). The animal may suffer death, anorexia (loss of appetite), dehydration, weight loss and diarrhoea, collectively leading to huge economic losses. There is considerable variation among lambs in susceptibility to infection. Much of the variation is genetic and influences the immune response.

There are a variety of ways to control the infection and a combination of control measures, for example genetic selection and vaccination, are likely to provide the most effective and sustainable control. To date, there are no licensed vaccines available for this parasite and treatment has relied on use of anthelmintics (parasiticides) for decades. The use of anthelmintics is not desirable as the parasites are becoming increasingly resistant to anthelmintics. The genetic intervention will perhaps provide the most promising and sustainable solution to control these infections. In this approach, a chromosome-length genome assembly will be crucial not only to understand the worm biology but to understand host-parasite interaction and to identify potential vaccine candidates.

DNA Zoo Australia has been working with Shamshad Ul Hassan, Emeritus Prof Graeme Martin, Adj/Prof Johan Greeff and team at The University of Western Australia (UWA) to deliver this much required key fundamental genomic resource. Here, we use in situ Hi-C to generate a chromosome-length assembly of T. circumcincta. The chromosome-length assembly we share today is based on a draft hybrid assembly published by Choi et al., 2017. The draft genome assembly was created using whole genome shotgun libraries (fragments and mean insert size of 3kb and 8kb) and assembled using Newbler v. 2.6 (Choi et al., 2017).

The above draft was run through purge haplotigs software (Roach et al., 2018) and scaffolded with 141,485,460 PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details! Visit the corresponding assembly page and check out the chromosomes below:

The Hi-C work was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

These new genomic tools and resources for T. circumcincta will enable detailed comparative genomic investigations of teladorsagiosis, better understand the parasite biology and evolution, interactions with host and potentially new molecular channels to intervene the infection process and to identify vaccine candiates.

The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, Shamshad Ul Hassan, Ashling Charles & Parwinder Kaur.

Blog by: Parwinder Kaur and Shamshad Ul Hassan.

Citations:

Choi, Y., Bisset, S.A., Doyle, S.R., Hallsworth-Pepin, K., Martin, J., Grant, W.N., Mitreva, M., 2017. Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta. Plos Genetics. https://doi.org/10.1371/journal.pgen.1006857

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.

Faster than Usain Bolt

The patas monkey, Erythrocebus patas, is the fastest monkey in the world! They're able to sprint from zero to 35 miles per hour in just 3 seconds [1]. In contrast, the world's fastest man, Usain Bolt, only reached speeds of 28.45 mph in 7 seconds in the 2008 Beijing Olympics [2]. Unlike many other monkeys, their slender bodies and long limbs are morphologically suited for terrestrial movement and speed rather than for arboreal movement.

The patas monkey usually lives in large, sexually segregated groups of around 40 to 60 individuals. The female troops are mostly female with one male who serves as a protector and occasionally a mate. Male monkeys live separately in their own groups of a similar size. During the breeding season, the male and female groups will meet and mate. While female patas monkeys stay in their troop for their whole lives, male patas will leave their maternal groups once they reach sexual maturity [3].

Patas monkey by Nik Barrow, [CC BY-NC 2.0], via flickr.com

Today, we release the chromosome-length genome assembly for the patas monkey. This is a $1K de novo genome assembly with a contig n50 = 55 KB and a scaffold n50 = 100 MB. For assembly procedure details, please check out our Methods page. We thank Cassie, the patas monkey at the Houston Zoo, for donating a blood sample for this genome assembly. Read more about Cassie here!

Check out below how the chromosomes in the new assembly relate to those of the olive baboon, a relatively close relative of the patas monkey with assembled chromosomes (genome assembly Panu_3.0 from the Human Genome Sequencing Center, ~10MY to common ancestor), and to human chromosomes (GRCh38, ~25MY to common ancestor).

Whole-genome alignment plot between Panu_3.0, a chromosome-length genome assembly for the olive baboon from HGSC, and Erythrocebus_patas_HiC, the patas monkey genome assembly.

Whole-genome alignment plot between the new patas monkey genome assembly (Erythrocebus_patas_HiC) and human chromosomes (hg38).

We're not monkeying around here at the DNA Zoo: this is the 10th primate species we've released on our website! If you're interested in more monkey genomes, check out, e.g. these pages for the Allen's swamp monkey and the Bolivian squirrel monkey, and don't forget to reach out if you have interesting primate samples!