The Australian lemming

They don’t jump of cliffs but eat grasses just like their Arctic relatives: meet the Tooarrana aka the broad-toothed rat aka Mastacomys fuscus!

Photo Description - Mastacomys fuscus, Broad-toothed Rat. Location: Australia, Victoria, Alpine National Park, Davies Plain. Survey: ALB 2013 0925. Alpine Bioscan. Photo Credits and acknowledgements - Source: Museums Victoria / Photographer: Heath Warwick

If you like to enjoy yourself by going for a walk near green vegetation, streams and waterfalls, you may find yourself share a similar taste with broad-toothed rat. These adorable creatures with a gentle demeanor are nocturnal medium-sized rodents with a short-tail, a broad face and a big belly. As a herbivore feeding mainly on stems, seeds of grasses and sedges, they are active in runways underneath the snow in the winter.

The animals thrive in alpine and sub-alpine areas and due to climate change have experienced a significant decline. As a result, the broad-toothed rat was classified as near threatened in the IUCN Red List of Threatened Species 2016.

Things have gotten even worse for Tooarrana after the catastrophic bushfire season 2019/2020. See below, for example, a photo of what was a thriving broad-toothed rat habitat for generations, now charred.

An image of what some of the broad-toothed rat sites in the burn scar looked like a few weeks ago, including the one in which the material for this study was collected. You can see the runways used by the rats for generations revealed on the charred ground, where before the fire they would have been covered by grasses, heath, and shrubs.

Under the Saving Our Species program, a targeted strategy for managing the broad-toothed rat has been developed, and DNA Zoo teamed up with Museums Victoria Senior Curator of Mammals Kevin C. Rowe and Oz Mammal Genomics to get a genome for the species assembled to help with the conservation efforts. Today, we are happy to release the chromosome-length assembly for the species.

The draft genome assembly was created using the wtdbg2 assembler (Ruan and Li, Nat Methods, 2019), using Oxford Nanopore reads (23.5Gbp, ~3.5 Million nanopore reads with read N50 of 15.9kb) polished with short-insert size Illumina reads (138Gbp, 459,921,452 PE 150bp).

The draft was scaffolded to 24 chromosomes using a total of 454,485,855 151bp PE Hi-C reads (137Gbp) using 3D-DNA and Juicebox Assembly Tools. See our Methods page for more detail!

Over the next year Museums Victoria will resequence 50 broad-toothed rat genomes and map them to the newly created reference. This will help monitor the population and inform the species management plans.

Read more about Tooarrana in this wonderful article by Joe Hinchliffe!

We gratefully acknowledge the collaboration and samples provided by Kevin C. Rowe, Museums Victoria. The sample generation for draft assembly was supported by Oz Mammals Genomics, a collaborative at Bioplatforms Australia initiative building genomic resources for Australian marsupials, bats & rodents. The draft genome assembly was supported by ShanghaiTech High Performing Computing Platform and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, China. The Hi-C work was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

The following people contributed to the project: Erez Aiden, Olga Dudchenko, Parwinder Kaur, Ruqayya Khan, Kevin Rowe, David Weisz & Zhenzhen Yang.

Blog by: Zhenzhen Yang & Parwinder Kaur

For more detail please visit https://www.dnazoo.org/assemblies/Mastacomys_fuscus

Citations

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.

Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.

Durand, Shamim et al. “Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.” Cell Systems 3.1 (2016): 95–98.

James T. Robinson, Douglass Turner, Neva C. Durand, Helga Thorvaldsdóttir, Jill P. Mesirov, Erez Lieberman Aiden, Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data, Cell Systems, Volume 6, Issue 2, 2018

Ruan, J. and Li, H. (2019) Fast and accurate long-read assembly with wtdbg2. Nat Methods doi:10.1038/s41592-019-0669-3

Earn your stripes!

Grant’s zebra (Equus quagga boehmi) is the smallest of the seven subspecies of the plains zebra (Equus quagga) aka the common zebra. In Africa, Grant’s zebras roam grasslands and savannahs, eating coarse grasses that other grazing animals may not ingest. Though there are more wild populations of Grant’s zebra than other zebra species, they are not immune to environmental threats. The IUCN categorizes Grant’s zebra as near threatened with its population in decline, mostly due to habitat loss for agricultural development and human conflicts in their regions.

Mother and foal, photo by Seth Eisenberg [CC BY-SA 4.0], via wikimedia.org

Of course, zebras are famous for their contrasting black and white stripes. Incredibly, there is still ongoing debate about why they sport their unusual striped pattern. Many functions have been proposed, including camouflage, repelling insects and thermoregulation [1,2,3].

Among some of the more recent findings on the matter of zebra striping is the correlation between the intensity and opacity of striping in zebras and their native environment’s temperature. Generally, zebra species that inhabit warmer climates have dark, broad stripes that cover most of their body. In the cooler regions near South Africa, the striping pattern is lighter, thinner, and may only cover the head and abdomen. Based on this finding, researches can now accurately predict what the zebras in different regions of Africa look like! Read more about this here.

The debate on how the zebra got its stripes goes all the way back to Charles Darwin and Alfred Russel Wallace. To bring in some genomics resources to weigh in on the question, we release today a de novo chromosome-length genome assembly for the Grant’s zebra. This is a $1K genome assembly with contig N50 = 89kb and scaffold N50 = 114Mb. This assembly was created with the help of two zebras: Ziggy from the Houston Zoo and Zena from Hearts and Hands Animal Rescue. Thank you, Nancy Nunke (Hearts and Hands Animal Rescue), Greg Barsh (Stanford University/Hudson Alpha) and Brenda Larison (UCLA) for their help with this assembly! Follow this link to visit the assembly page.

See below how the Grant zebra’s chromosomes relate to those of a domestic horse. That’s a lot of rearrangements for only ~4 million years separating the species! (Compare this, for example, to the very stable chromosomes in the cat family.)

Whole-genome alignment of the Grant’s zebra assembly (Equus_quagga_boehmi) to the domestic horse (EquCab2.0).

Post by: Ruqayya Khan, Olga Dudchenko

P.S.: If you have ever wondered if the zebras are black with white stripes or white with black stripes, wonder no more; the questions has finally been definitively answered!

P.P.S.: Since Grant's derives from a subspecies designation and subspecific designations are somewhat dubious, on the assembly page we refer to the species as plains zebra.

A Parasitic flatworm infecting over 15 million with no vaccine

Parasitic flatworms cause substantial death and disease in humans. The Chinese liver fluke, Clonorchis sinensis, is one of the most destructive parasitic worms in humans in China, Vietnam, Korea and the Russian Far East. Read more about Chinese liver flukes on Wikipedia.

Banchob Sripa, Sasithorn Kaewkes, Paiboon Sithithaworn, Eimorn Mairiang, Thewarach Laha, Michael Smout, Chawalit Pairojkul, Vajaraphongsa Bhudhisawasdi, Smarn Tesana, Bandit Thinkamrop, Jeffrey M. Bethony, Alex Loukas & Paul J. Brindley / CC BY (https://creativecommons.org/licenses/by/2.5)

Although C. sinensis infection can be controlled relatively well using drugs (anthelmintics), the worm can cause cancer (cholangiocarcinoma) and causes major suffering in ~ 15 million people infected in Asia. No vaccine is available to prevent parasite infection, and humans have no resistance to reinfection.

To better control this flatworm, research has been conducted on the molecular biology of the parasite, focused on diagnosis and treatment. A deep understanding of the fluke’s molecular biology is underpinned by characterizing its genome. Today, we release an chromosome-length genome assembly for C. sinensis, produced using our existing short read assembly and new Hi-C data. The new assembly will provide a basis to conduct in-depth molecular studies of C. sinensis and broader comparative genomics and genetics of flatworms.

Read more here: Wang D, Young ND, Korhonen PK, Gasser RB. Clonorchis sinensis and Clonorchiasis: The Relevance of Exploring Genetic Variation. Adv Parasitol. 2018;100:155-208.

For the draft assembly used for this effort, please cite the following:

Wang D, Korhonen PK, Gasser RB, Young ND. Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications. Biotechnol Adv. 2018;36(4):894-904.

Acknowledgments:

We gratefully acknowledge the collaboration and samples provided Dr. Neil Young, The University of Melbourne. This work was supported in part by resources provided by DNA Zoo Australia, The University of Western Australia (UWA), with compute resource and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.