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!

DNA Zoo Australia intern Ashling Charles bags Pawsey People’s Choice Award for 2020

DNA Zoo Australia offered two projects this year collaborating with the Pawsey Supercomputing Centre Summer Internship program. This program is designed to enable undergraduate students to develop skills in computational science by giving students the opportunity to immerse themselves in advanced computing research projects. Interns were  supervised by DNA Zoo teams from Perth and Houston and undertook challenging research projects utilizing the resources provided by the Pawsey Supercomputing Centre.

DNA Zoo teams provided the genomes datasets and Pawsey provided access to high-performance computing, visualization facilities, large-scale data storage and high-speed communications along with expert help from both teams to make the best use of technology.

Ashling Charles, conducted research into the genomic alignment of DNA Zoo assemblies towards Mapping conservation in the human genome with single-base-pair resolution. The key was to find a proficient solution to aligning mammalian genomes for comparative analyses. CACTUS; a reference-free whole-genome multiple alignment program was selected for investigation. Ashling focused on conducting the preliminary testing and implementation of the software package for DNA Zoo genome data.

PAWSEY held an evening event where each intern presented their research, all relating to computational science. Ashling won the People’s Choice Award for her presentation on CACTUS. We are thrilled by this response and hope to further our efforts towards the rapid generation and release of high-quality genomic resources. 

Ashling's poster can be found here: https://www.dropbox.com/sh/jc96mrizfc1oguu/AABNNxWRO69C4toEniBL-jfja?dl=0