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.

The very hairy not so scary

In the lowland forests of the Congo Basin, Allen’s swamp monkeys (Allenopithecus nigroviridis) may be found foraging for fruit, insects, and leaves. A member of the Old-World monkey family, Allen’s swamp monkey is classified in its own genus, Allenopithecus. This species was named after the renowned American zoologist, Joel Asaph Allen.

Allen’s swamp monkey (Allenopithecus nigroviridis), Photo by Heather Paul [CC BY-ND 2.0], via flickr.com

As their name suggests, these monkeys inhabit swamps and marshes. Their hands and feet are slightly webbed, making them strong swimmers. The swamp monkey may dive into water to avoid predator’s attacks. In the wild, the predators of the swamp monkey are falcons, snakes, and larger primates such as the bonobo. The Allen’s swamp monkey is also hunted for its meat by humans and sold in local markets. 

Today, we are releasing the chromosome length assembly of Allen’s swamp monkey. This assembly was prepared from two monkeys from the Houston Zoo, Ota and Pepper. Read about Pepper here in the Houston Zoo’s blog post, Points on Pepper! She is the daughter of a wild born monkey Naku, who was rescued in 2003 from an African market.

This is a $1K-model genome assembly, with contig N50=48kb and scaffold N50=115Mb. See Dudchenko et al., 2018 for more details on the methodology!