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.

Hogs and kisses

The North Sulawesi babirusa (Babyrousa celebensis) is a member of the Suidae family native to swampy forests of Indonesia. Their famous tusks have inspired generations of art and folklore in Indonesia, where the tusks of the babirusa are often featured in traditional masks. The upper tusks of male babirusas will continue to grow throughout their lifetime, eventually curling over the head if not worn down through fights with other males. Female babirusas are easy to identify as they lack upper tusks [1]. Babirusas are great swimmers and spend much of their time wallowing in the mud to keep cool and protect their skin.

Due to deforestation of the natural habit and excessive hunting, the wild population of the babirusa is drastically declining. The ICUN Redlist has categorized the Sulawesi babirusa as vulnerable. As babirusas do not easily breed in captivity, breeding programs haven't been able to keep up with the rate of decline of the wild population.

North Sulawesi Babirusa (Babyrousa celebensis) by Josh More, [CC BY-NC-ND 2.0], via flickr.com

Today, we share the chromosome-length assembly for the North Sulawesi babirusa, Babyrousa celebensis. This is a $1K de novo genome assembly, with a contig n50 of 53 Kb and a scaffold n50 of 113 Mb. For details on assembly procedure, check out Dudchenko et al., 2018 or our Methods page. We thank Remley from the Houston Zoo for providing the sample that has made this genome assembly possible! Read more about Remley and her partner Jambi in this featured blog post by the Houston Zoo celebrating National Pig Day (March 1st).

Check out how the chromosomes in the new assembly align with those of the domestic pig Sus scrofa (assembly by Warr et al., 2020) in a whole-genome alignment plot below. While both of these Suidae species have a karyotype of 2n=38, there are considerable differences including two chromosome breakages (#3 and #6 in the domestic pig), two fusions (#13+#16; #15+#17 in domestic pig) and a big inversion on the pig chromosome #1 equivalent.

Whole genome alignment plot between the babirusa (Babyrousa_celebensis_HiC) and the domestic pig (Sscrofa11.1)

Interestingly, in 2006, a zoo in Copenhagen managed to cross a different babirusa species (B. babyrussa) with the domestic pig, leading to hybrid offspring [2]. Previously thought to be sexually incompatible due to genetic distance of the species, the cross produced three surviving offspring. The hybrids were sterile though, which is probably at least in part due to chromosomal differences between the crossed species similar to the one shown above. Reach out if you have a B. babyrussa sample to confirm!

Chromosome-length assembly of Schistosoma haematobium

Schistosoma haematobium (blood fluke or schistosome) is a flatworm parasite that infects humans in Africa and the Middle East. It is one of three main blood flukes causing schistosomiasis, a neglected tropical disease that affects more than 200 million people worldwide.

Histopathology of Schistosomiasis haematobia by Dr. Edwin P. Ewing, Jr. (CDC), [Public Domain], via wikimedia.org

Unlike the other two species, S. haematobium adults prefer to migrate to blood vessels surrounding the bladder and genitals (urogenital system). Disease results principally from a chronic inflammatory process directed at schistosome eggs that become entrapped in urogenital tissues, and is often accompanied by increased susceptibility to HIV/AIDS in women or by malignant bladder cancer.

There is no effective vaccine to protect humans and control currently relies heavily on targeted or mass treatment with a drug called praziquantel (PZQ). The widespread use of PZQ potentially promotes resistance in schistosomes. Therefore, there is a major imperative to develop a new generation of interventions, built on a deep knowledge and understanding of schistosome genetics, biology and the pathogenesis of disease. The complex genetics of blood flukes have confounded efforts to achieve these goals. For example, S. haematobium is known to hybridise with other blood fluke species (e.g. Schistosoma bovis), resulting in viable offspring with unknown traits. To investigate the impact of past introgression and/or recent hybridisation events, the research community requires reference-level genome assemblies for blood flukes.

DNA Zoo has been working with Dr. Neil Young and team at The University of Melbourne, Australia to deliver this much required key fundamental genomic resource. Here, we use in situ Hi-C to complete a chromosome-length assembly of S. haematobium. The chromosome-length assembly we share today is based on a draft hybrid assembly generated by Neil Young, Andreas Stroehlein, Pasi Korhnonen and Robin Gasser at the University of Melbourne. The draft genome assembly was created using existing short-read Illumina and Dovetail sequence libraries and new Oxford Nanopore long-read data. Genomic data was created with support from the National Health and Medical Council and Australian Research Council.

The above draft was scaffolded into 8 chromosomes (see contact map below) with 30,735,883 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.

These new genomic tools and resources for Schistosoma haematobium will enable detailed comparative genomic investigations of schistosomes, improve our understanding of urogenital schistosomiasis and assist in developing a new generation of interventions against schistosomes.

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

Blog by: Parwinder Kaur and Neil Young