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

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).