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.
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.
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.