A claw-some species

As the name suggests, the Asian Small-Clawed Otter (Aonyx cinereus) is the smallest of all otter species and inhabits parts of Asia, like Indonesia, southern India, China, and the Philippines. As semiaquatic mammals, they call rivers, streams, and even mangroves home. To facilitate life underwater, these otters are able to close both their nostrils and ears while swimming! [1]

Uniquely, Asian small-clawed otters use the webbing between their toes to locate and trap food instead of their mouths. Despite the small size of their paws, these otters are able to crush the shells of crabs and mollusks with their paws. When that isn’t possible, they cleverly wait for the heat from the sun to break open the shells and access the meat [2].

This is especially different from their otter relatives, like the Northern River Otter (Lontra canadensis), who exclusively capture prey using their mouths! (You can learn more about the Northern River Otter in a previous blog post.)

Photograph by Jen Zoon, Smithsonian’s National Zoo [CC BY-NC-ND 2.0], via flickr.com

Asian small-clawed otters are heavily social, and typically exist in groups of 15-20 individuals. If you are ever around a family of these otters, you are likely to hear their many sounds, used for greeting, play, contact and alarm, as they are an extremely vocal species! Although this hasn’t been formally studied, many agree that they are incredibly otterable and very camera-friendly!

Sadly, Asian small-clawed otter populations have been slowly declining as a result of pollution, loss of habitat, and hunting. Which is why they are now considered a Vulnerable species by the International Union for Conservation of Nature (IUCN) [3]. Given that the biggest threat to their populations is loss of habitat and prey from pollution, there are simple things we can do to help this species. According to the Smithsonian, practicing the 3-Rs: Reduce, Reuse, Recycle (in that order), is an effective way of decreasing pollution and disturbance to the habitats of these Asian small-clawed otters. [4]

Today, we release the chromosome-length assembly for this otterly cute species. This is a de novo $1K genome assembly with contig N50 = 69 kb and scaffold N50 = 131 Mb. See Dudchenko et al., 2018 for details on the procedure.

For this genome assembly, we have used two samples from our collection. For DNA-Seq, the used blood donated by Hope, the small-clawed otter at the Houston Zoo. (Read more about Hope and her partner Danh Tu in this post by the Houston Zoo.) A blood donation from another otter, from San Antonio Zoo, was used to generate the Hi-C data for chromosome-length scaffolding. Thanks!

New wave of Beetlemania

Today, we release a few improvements to a pioneering genome, Tribolium castaneum (Herbst) 1797.

The red flour beetle (RFB), is a member of the Order Coleoptera, aka beetles, one of the most diverse group of organisms on earth (~400,000 species). Within Coleoptera, the RFB is a member of the family Tenebrionidae, which itself is exceptionally diverse with ~20,000 species. Tenebrionidae are colloquially referred to as tenebs or darkling beetles by Coleopterists and can be found almost everywhere. Some can be omnivorous as larvae and adults but others are specialized on eating fungus for their development (mycetobionts/fungivores).

The RFB has become a stored product pest, originally believed to be native to SE Asia. Now it can now be found worldwide as a result of it hitching rides in product such as (you guessed it) flour.

Red Flour Beetle (Tribolium castaneum) by Udo Schmidt [CC BY-SA 2.0], via flickr.com

Many tenebrionids are found in arid environments but other members of this family are diverse in tropical regions. One of their larval adaptations for surviving in exceptionally dry environments is the modification of the Malpighian tubules (rough insect equivalent of your kidneys) into what is termed a cryptonephridium, where they can not only draw out water from their excrement but also absorb atmospheric water trapped in their hindgut.

Many but not all tenebrionid adults have abdominal glands that produce noxious quinones as defensive chemicals, (RFB specifically produces p-benzoquinones with aliphatic hydrocarbons). If you live in North America and have picked up one of these, you will know what we are talking about. As a result of this noxious defensive which is physiologically expensive to produce, some tenebs have a convergent appearance falsely advertising “Don’t eat me I taste bad!”, mimicking the distasteful species.

The RFB was the first beetle to have its genome sequenced and has been the genetic workhorse of Coleoptera. This was done back in 2008 by the Tribolium Genome Sequencing Consortium. Subsequent improvements include Kim et al., 2010 and Herndon et al., 2020. This latter version, available on NCBI here, is used as a starting point for the Hi-C based upgrade. The sample for Hi-C library preparation was obtained from Carolina Biological.

Blog post by Matthew Van Dam

Citations: 

Herndon, N., Shelton, J., Gerischer, L.et al.Enhanced genome assembly and a new official gene set forTribolium castaneum.BMC Genomics21,47 (2020). https://doi.org/10.1186/s12864-019-6394-6

Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, et al. (April 2008). "The genome of the model beetle and pest Tribolium castaneum". Nature. 452 (7190): 949–55. Bibcode:2008Natur.452..949R. doi:10.1038/nature06784. PMID 18362917

Shimeld, Lisa Anne, "A cytogenetic examination of eight species of Tribolium (Coleoptera: Tenebrionidae)" (1989). Theses Digitization Project. 534. https://scholarworks.lib.csusb.edu/etd-project/534

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