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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

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

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