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!

A bat that grows on trees

- Fondly referred to by some of the scientists chasing them around North America as “sky lions”, hoary bats Aeorestes cinereus are the among the biggest, flashiest, and widest ranging bats on the continent.

Hoary bat (Lasiurus cinereus) - pregnant female resting in a tree during spring migration. Photo by Paul Cryan.

- Unlike a lot of the other 40+ species of bats occurring in the U.S. & Canada, they have bright markings and contrasting colors (e.g., wing spots, yellow fur on inside of underwing and ringing their face and ears, reddish pink skin on the tops of their wings).

- Unlike a lot of other bats ranging into the temperate North America, they spend most of their lives in trees, sometimes maybe hiding under leaf litter on the ground during colder months.

- These are definitely not cave bats, because they actually get lost and die within caves when they happen to wander in.

- We don’t know much about the details of their seasonal movements, but they are highly migratory and seem to always be on the move (individuals probably migrate up to a couple thousand kilometers each way).

- They may be the widest ranging of all the terrestrial mammals in North America other than humans (I say terrestrial because whales, dolphins, and other marine mammals may migrate similar or longer distances).

- We don’t really know where the bulk of the North American population spends the winter, probably because they migrate to wintering grounds and then hibernate, which is typical bat weird/amazing.

- Our best guess is that females migrate about a month before males in spring out of wintering grounds in coastal California and Mexico, then move to summering grounds east of the Rockies where they birth and raise their pups.

- This is one of the few bats in North America in which females consistently gives birth to more than a single pup each year---twins seem to be the norm, but triplets and quadruplets aren’t that unusual.

- A mother an her pups is about as big a social groups get with hoary bats, which is why we in the business refer to them as ‘solitary tree bats.’

- Males are typical and migrate about a month later than females in the spring, mostly stop in the Rocky Mountains for the early summer, and don’t seem to travel nearly as far as the females during the spring and early summer.

- Things start to get strange and tragic as the females and their volant young start heading back to the wintering grounds in late summer and autumn.

- For reasons we still don’t quite understand, hoary bats compose about half of the tens of thousands of bats estimated to be dying after colliding with the blades of wind turbines each year.

- Most bat fatalities at wind turbines happen between about mid-July and early October, which is when the females and their young are heading back toward the wintering grounds and the males are dispersing out of their different summering areas to try and intercept females to mate with before they hunker down for the winter.

- Like most bats, hoary bats mate in the autumn and winter, then females store the sperm and fertilize themselves to be independent of the males in spring.

- The particular susceptibility of hoary bats to wind turbines might have something to do with their mating behaviors (and striking colors), but that is still mostly speculation, see here.

- Hoary bats mate by somehow finding each other while migrating in the dark, then the act begins in flight, with the couples falling to the ground as it commences.

- Our best guess right now is that hoary bats visually mistake (echolocation only works out to about 100 m and they have very sensitive but fuzzy night vision) the silhouettes of wind turbines for the trunks and crowns of large trees, then approach expecting to find something they need there, like insect accumulations, friends/mates, or simply places to rest.

- Some of us tracked a few hoary bats with GPS tags and followed one male making a 1000-km circular trip from the redwood forests of central California up to Oregon, Nevada, and then back to California in a few weeks during October, see here.

- We also put some custom-made dataloggers that recorded temperature, light levels, acceleration, etc. on hoary bats and caught one hibernating in a tree all winter in a redwood forest of CA (see here).

- Details of how hoary bats hibernate are not known, but their scientific name (at least the one I grew up with), Lasiurus cinereus, roughly translates to hairy tailed and ash colored; when they get really cold they roll up into a furry ball (I’ve heard anecdotes about hoary bats being found balled up under snow in mountains of Arizona, but it hasn’t been clearly documented yet…but a morphologically similar species in Japan hibernates under the snow - read here).

- As far as I can tell, the newly proposed genus name Aeorestes translates from Latin to something like ‘an eater that flits about.’

- Hoary bats made it out to Hawaii a couple times in the past, and were the only terrestrial mammal (again, marine mammals were there) occurring on the archipelago when humans arrived (read about it here).

- Today, we release a chromosome-length genome assembly for the hoary bat, based on the draft generated by the United States Geological Survey (Cornman, R., Cryan, P., Fike, J. and Oyler-Mccance, S., 2020). The sample used for Hi-C library preparation was collected in Fort Collins, Colorado in September 2019, by Paul Cryan, USGS Fort Collins Science Center under Colorado Parks and Wildlife Scientific Collection License 19TR2010 from a recently deceased bat provided by Larimer County Public Health Department.