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

Mule deer

The mule deer (Odocoileus hemionus) is a species of Cervidae native to Western North America. They occupy a variety of habitats, from high mountain ecosystems to sagebrush deserts. Because their habitat is vast, their herbivorous diet consists of a large variety of plants. Mule deer are an iconic species of the Western United States and are important to the survival of many other species in the ecosystems in which they reside, as they are a primary food source for many of North America’s large predator species, such as pumas, coyotes, bears, and wolves.[i]

Mule deer on winter range Southwest Wyoming by USFWS Mountain-Prairie, [CC BY 2.0], via flickr.com

Mule deer are well-known for their striking antlers, the bony protrusions that rise out of the top of the skulls of males. Their antlers are one of their more definitive features and differ in branching pattern from the closely related whitetail deer. Mule deer antlers grow in an annual cycle, starting in the late spring when the antlers begin to form, and ending in the early fall when increased levels of testosterone hardens the antlers. After mating, reduced testosterone levels cause the antlers to fall off. Antlers are important for a variety of reasons, including defense, and acquisition of mating opportunities.[ii]

We are excited today to present a de novo chromosome-length genome assembly of the mule deer with chromosome-length scaffolding. A research team from two labs at Brigham Young University (Sydney Lamb, Tabitha Hughes, Randy Larsen, and Brock McMillan https://pws.byu.edu/wildlife-ecology and Adam Taylor and Paul Frandsen https://frandsen.byu.edu) generated the de novo draft genome assembly using high coverage PacBio and Illumina sequencing while DNA Zoo completed a Hi-C experiment to provide chromosome-level information. The genome was assembled using RedBean, followed by two rounds of polishing with Racon (PacBio reads) and Pilon (Illumina reads, fix-indels only), and finally 3D-DNA and Juicebox Assembly Tools for the Hi-C part (see dnazoo.org/methods). Check out the chromosomes below!

A paper describing genome assembly and annotation description is in the process of being written and will be made available as a preprint soon, but we wanted to make the genome assembly available as soon as possible for use in the community. In some areas, mule deer populations are in decline. Possible reasons for the decline include habitat loss, collisions with vehicles, predation, and the rising spread of Chronic Wasting Disease (CWD)[iii]. We hope this reference genome will provide genomic resources that will help in monitoring and management efforts across the species range. We express our gratitude to the Utah Division of Wildlife Resources for providing the tissue of the specimen that was used for this project.

Blog post by: Adam M. Taylor, Sydney Lamb, & Tabitha Hughes

[i] DeVivo, M. T. et al. Endemic chronic wasting disease causes mule deer population decline in Wyoming. PLoS One 12, (2017).

[ii] Wang, Y. et al. Genetic basis of ruminant headgear and rapid antler regeneration. Science 364, (2019).

[iii] Madson, Icon of the American West: Science Reference Center. National Wildlife (World Edition) 53, 26–29 (2014).

Nemesis and savior

The pine marten (Martes martes) is a medium-sized carnivore from the weasel family (Mustelidae); It is somewhat smaller than a house cat, normally weighing around one kilogram, with a slim, flexible body, strong springy limbs and long tail. It is generally brownish – anywhere from chocolate to tan – with a large contrasting yellowish patch on its neck. In winter, it grows thick, soft fur, which is why it has been among the most important furbearing species for centuries. It has an extensive range, stretching from Western Europe, including some of the British Isles, to the east across the Urals, reaching the Siberian rivers Irtysh and upper Ob; beyond that, it is replaced by its close relative, the sable (Martes zibellina), which occupies a very similar ecological niche. It is critically endangered in England and Wales, but is generally treated as Least Concern by IUCN. The pine marten is a fast and tenacious predator, targeting a variety of animals, from frogs, rodents and shrews to large birds, such as the capercaillie (Tetrao urogallus) – a strong, turkey-sized grouse. It also eats fruits, nuts, insects – and it is a notorious nest robber.

Pine marten by Caroline Legg, [CC BY 2.0], via flickr.com

The pine marten has likely co-evolved with its main prey, the red squirrel (Sciurus vulgaris) – its excellent vestibular apparatus, semi-retractable claws, and long, bushy tail with longer guard hair than in any other marten are adaptations to fast-paced arboreal hunts. However, in one part of its range, it has become the savior of the squiggly reds. In Scotland, the red squirrel was pushed away from its original habitats by the larger, more aggressive grey squirrels (Sciurus carolinensis) – an introduced North American species. The tables turned when the pine marten, previously nearly eradicated by local gamekeepers for the sake of grouse hunters, made a comeback to its former range after the species was granted full protection in 1988. Since red squirrels are generally on a par with their nemesis in terms of tree top acrobatics, martens opted for easier prey and feast on the heavier, slower greys, clearing out the living space for the reds.

We present the chromosome-length assembly for yet another – but not the final – species in the genus Martes. All C-scaffolds (Lewin et al. 2019) of the pine marten were assigned to the corresponding chromosomes via a Zoo-FISH experiment with the stone marten chromosomes used as probes. Both the stone and pine marten have the same diploid number of chromosomes (2n=38) with no detected translocations, so we arranged the pine marten chromosomes in the same order as in the stone marten karyotype. Among other types of rearrangements only several inversions were found (Fig. 1).

Figure 1. Whole genome alignment plot for the pine marten (mmar.min_150.pseudohap2.1_HiC) to the stone marten (mfoi.min_150.pseudohap2.1_HiC)

We thank Dr. Rogell Powell (North Carolina State University) for funding 10x Genomics linked-read sequencing for the draft assembly and Dr. Klaus Koepfli for organizing this sequencing and bringing all of the collaborators together. Also we thank Sergei Pisarev, Pavel Reznichenko and Ksenia Koniaeva from the zoo “Lesnaya skazka” (eng. “Forest tale”) in Barnaul, Russia, who provided samples for a cell line. These cells were used for both DNA extraction for linked read sequencing and for HiC experiments. DNA extraction and Zoo-FISH experiments were performed by Natalia Serdyukova and Dr. Violetta Beklemisheva. The initial assembly was performed by Sergei Kliver. Hi-C experiments and scaffolding to chromosomes were done by Polina Perelman, Ruqayya Khan, David Weisz and Olga Dudchenko. The genome annotation and a paper describing this research is in progress.

Citations:

Lewin, Harris A et al. 2019. “Precision Nomenclature for the New Genomics.” GigaScience 8(8): giz086.