The three muskaroos

Today, DNA Zoo Australia is celebrating!!! We are very happy to announce the receipt of funding from Lotterywest to build a comprehensive genomic resource especially for Western Australia, the WA Genome Atlas.

Australia is one of 17 “megadiverse” countries that comprise a large proportion of the Earth’s biological diversity and house a multitude of unique and endemic species. Southwest Australia specifically is the world’s first recognised global biodiversity hotspot. The WA Genome Atlas initiative supported by Lotterywest will establish a transdisciplinary hub of excellence to genetically characterise, record and support our unique biodiversity, and fill a gap in genetic knowledge required for ambitious ecosystem and species conservation.

To mark the occasion, the DNA Zoo is releasing the world’s first chromosome-length genome assemblies for three marsupials, the Western brush wallaby (Notamacropus irma) endemic to Western Australia, and it's cousins the swamp wallaby (Wallabia bicolor) and Matschie's tree-kangaroo (Dendrolagus matschiei)!

Photo collage featuring the Western brush wallaby photo by Jukka Jantunen, CC BY-NC 4.0; Swamp wallaby photo by James Bailey, CC BY-NC 4.0 and Matschie's tree-kangaroo photo by Wally Gobetz, CC BY-NC-ND 2.0 [www.flickr.com]

The western brush-wallaby (Notamacropus irma) used to be very common in Western Australia but hunting for its pelt by early settlers and habitat destruction has resulted in reduced numbers. Sadly, these wallabies are most commonly seen around the outskirts of Perth – lying on the side of the road after being struck by a car. Several orphaned joeys have been taken to Perth Zoo after their mothers were killed on roads. (Please take extra care when driving near bushland, especially at dusk and dawn!)

Visit the assembly page for Notamacropus irma here and browse the contact matrix for the eight chromosomes below. Thanks to Natasha Tay, Harry Butler Institute, Murdoch University, for assistance with the sample!

The swamp wallaby (Wallabia bicolor) is a small, stocky wallaby with dark brown fur, often with lighter rusty patches on the belly, chest and base of the ears. Its population is similarly decreasing due to habitat destruction and, to a lesser degree, killing by farmers. Fortunately, Wallabia bicolor is still common, and the issues it faces are not currently considered threats to its survival. Several physical and behavioral characteristics make the swamp wallaby different enough from other wallabies that it is currently placed apart in its own genus, but its phylogenetic placement is debated. We hope the chromosome-length genome assembly we present today will help to resolve this controversial taxonomy for the species.

Visit the assembly page for Wallabia bicolor here and browse the contact matrix for the five chromosomes below. Thanks to Ranger Red’s Zoo & Conservation Park for their help with the sample used for this assembly!

Finally, give it up for the Matschie's tree-kangaroo (Dendrolagus matschiei), a strikingly beautiful endangered tree kangaroo found only in Papua New Guinea. Habitat loss and over harvesting are the main threats to the species. We are happy to have an opportunity to add a chromosome-length genome assembly to support the research on Matschie's tree-kangaroo!

Check out the assembly page for Dendrolagus matschiei here, and browse the contact matrix for the seven chromosomes below. We are grateful to the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center that contributed the fibroblasts for this genome assembly.

This work was enabled 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. The WA Genome Atlas project leading the West Australian node of the global DNA Zoo initiative is proudly supported by Lotterywest.

The mane of the hour

Much like a lion's mane, the golden-headed lion tamarin, Leontopithecus chrysomelas, has a brilliant display of orange fur framing their face. This mane wonderfully contrasts the black fur of their bodies, not to be confused with the golden lion tamarin (L. rosalia) which is completely gold all over. The golden-headed lion tamarin is one of four species of tamarin, found only in the tropical rainforests of Brazil. Unfortunately, due to major deforestation and loss of habitat, all four species are considered endangered [1].

Leontopithecus chrysomelas by Hans Hillewaert, [CC BY-NC-ND 2.0], via flickr.com

Like many primate species, golden-headed lion tamarins are social animals that live in groups of 2-11 individuals. Twins are the most common offspring for the golden-headed lion tamarins, while single, triplet, and quadruplet offspring being less common [2]. As for raising their young, both parents tend to take an equal role in child rearing.

Today, we release the chromosome-length assembly of the golden-headed lion tamarin, Leontopithecus chrysomelas! This is another $1K genome assembly, with a contig n50 = 48 KB and a scaffold n50 = 118 MB. For procedure details see Dudchenko et al., 2018 and our Methods page. We thank twin siblings Maya and Marcos from the Houston Zoo for providing the material used to generate this genome assembly. Read more about Maya and Marcos in this blog post by the Houston Zoo!

This genome marks the 25th primate we've released on the DNA Zoo blog, browse our other releases here! Finally, check out the 23 chromosomes of golden-headed lion tamarin in the interactive Juicebox.js session below:

Sand flies: very small disease vectors

Blood feeding insects that feed on multiple people can spread disease. Mosquitoes are one example where the female mosquito requires a blood meal for protein to properly grow and lay her eggs. This act of blood feeding spreads the malaria parasites to and between people. Another example are sand flies. Sand flies, about ¼ the size of a mosquito, are tiny insect vectors of a different parasite – Leishmania.

Leishmaniasis is the second biggest parasitic killer after malaria. It is estimated to kill around 40,000 people every year, and accounts for about 2.4 million disability-adjusted life-years (DALYs). The Leishmania parasite is transmitted to humans when female sand flies bite humans to obtain blood meals that they require for reproduction. As of August 2022 (the time of writing), there is an outbreak of cutaneous leishmaniasis in Syria near a polluted and drying up river – as reported by VOA news here.

Current treatments of leishmaniasis are highly toxic and/or expensive and no efficacious vaccine exists. Therefore control of this disease requires controlling the Phlebotomine sand flies that transmit Leishmania parasites. A better understanding of sand fly biology and populations is necessary for the control and monitoring of the disease.

Today, we share two chromosome length assemblies for these two sandfly species: Phlebotomus papatasi and Lutzomyia longipalpis. P. papatasi is a vector of the cutaneous leishmaniasis causing parasite Leishmania major in the Old World. L. longipalpis is a vector transmitting Leishmania infantum that causes visceral leishmaniasis in South America.

Left: Lutzomyia longipalpis sandfly by Ray Wilson, (2009) PLoS Pathogens Issue Image - Vol. 5(8) August 2009. PLoS Pathog 5(8): ev05.i08. doi:10.1371/image.ppat.v05.i08, [CC BY 4.0]. Right: Phlebotomus papatasi sandfly by Frank Collins, Centers for Disease Control and Prevention's Public Health Image Library (PHIL), identification number #10277, [public domain].

It is our hope that these new high quality reference genomes will enable new and improve ongoing methods of integrated vector control. The improved genome assemblies should enable complex genetic analyses, including descriptions of species complexes, estimation of effective population sizes, monitoring of pesticide resistance allele emergence, and hopefully eventually lead to new leishmaniasis-control methods. Recently, new mosquito genomic resources enabled new vector control methods such as CRISPR-Cas9-based manipulation that create gene drives to prevent malaria transmission and microbiome manipulation with Wolbachia to prevent transmission of dengue. We hope that new reference genomes will enable similar innovative approaches to be developed for sand flies.

The extremely small size of the sand fly made generating these genomes a challenge. Only about 30-50 nanograms of DNA can be isolated from a single male sandfly (males are used here to characterize both the X and the Y sex chromosomes). Using pooled samples and older sequencing technologies in the early sequencing attempts produced extremely fragmented assemblies. We would like to thank researchers at Pacific Biosciences for using these species as a test for their new ultra-low input library generation protocol for the HiFi sequencing technology. When combined with the Hi-C magic performed by the DNA Zoo, we now have highly accurate contiguous sequences scaffolded to chromosome lengths that should stand as a reference for future leishmaniasis prevention research for years to come.

Data from two PacBio Sequel II SMRT cells generated at the BYU sequencing center was assembled with hifiasm (Cheng et al., 2021). Pacific Biosciences generated HiFi data for Phlebotomus papatasi, the draft assembly for was generated by Dr. Sarah Kingan at Pacific Biosciences. For Lutzomyia longipalpis, Sequel II Hifi Data was generated by Oanh Nguyen at the UC Davis Genome Center from a single male using the ultra-low input DNA library kit generated by Dr Kingan and Colleagues at PacBio, and the initial assembly was performed by Stephen Richards using hifiiasm. These high-quality drafts were upgraded to chromosome-length assemblies using Hi-C data from multiple male individuals from the colonies at The University of Notre Dame maintained by Drs. Mary Ann McDowell and Douglas Shoue.

Check out the interactive Juicebox.js instance below for a contact map of five P. papatasi and four L. longipalpis chromosomes, and visit the assembly pages (here and here) for more information and details on the procedure. The genome assemblies are also available on NCBI as Ppap_2.0 (P. papatasi) and ASM2433408v1 (L. longipalpis).

Blog post by Stephen Richards and Mary Ann McDowell.