Ain't no mountain high enough

Mountain zebras (Equus zebra), endemic to South Africa and Namibia, are one of three extant species of extant zebras and comprise two recognized subspecies, the Cape mountain zebra (E. z. zebra) and Hartmann’s mountain zebra (E. z. hartmannae). Like their sister species, plains and Grevy’s zebras, they are recognizable by their iconic black and white stripes. Mountain zebras fall between the other two species in size and the thickness of their stripes. Mountain zebras can also easily be distinguished by the fact that they possess a dewlap, a fold of skin hanging from the throat.

As their name implies, they prefer mountainous terrain up to about 3000 feet. Once listed as endangered (IUCN Red List - 1996) with a global population of between 2-3000 only 80 of which were Cape mountain zebra, the species has rebounded to a global population of 35,000, 1700 being the Cape subspecies. They are still vulnerable, however, due to habitat fragmentation and the potential threat of increased drought due to climate change. It was drought that caused the catastrophic decline that led to the population nadir in the 1980’s.

Mountain Zebra stallion by Bernard Dupont, [CC BY-SA 2.0], via flickr.com

Today we share the $1K assembly of the mountain zebra. The sample for the assembly was provided by a mountain zebra named Zakota and obtained by Greg Barsh (Hudson Alpha/ Stanford University) and Ren Larison (UCLA) during a visit to the Hearts and Hands Animal Rescue in Ramona, CA, owned by animal lover and zebra whisperer Nancy Nunke. During our visit Nancy had us stroke the fur along the back of a mountain zebra, allowing us to learn an unusual fact about them; the fur between the saddle and rump grows backward, with the nap back to front instead of front to back.

Like the plains zebra, the mountain zebra shows quite a bit of rearrangement in their chromosomes relative to the domestic horse (see whole genome alignment plots below). This rearrangement is also reflected in the large differences in number chromosomes among the three species, with the horse having 32 pairs of chromosomes, the plains zebra 22, and the mountain zebra only 16 – half that of the horse. In spite of these re-arrangements equids are notorious for their ability to hybridize, leading to the fascinating pelage patterns seen in hebras and zorses, as well as potential conservation threats due to hybridization between the rarer zebra species - mountain zebras and Grevy’s zebras - and the vastly more common plains zebra.

Whole-genome alignment between the new chromosome-length genome assembly for the mountain zebra (Equus_zebra_HiC) and that of the domestic horse (EquCab2.0, from Wade et al., Science 2009).

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