Chromosome-length genome assembly of Teladorsagia circumcincta - a globally important helminth parasite in livestock

Shamshad Ul Hassan; Eng Guan Chua; Erwin A Paz; Chin Yen Tay; Johan C Greeff; Dieter G Palmer; Olga Dudchenko; Erez Lieberman Aiden; Graeme B Martin; Parwinder Kaur

doi:10.1186/s12864-023-09172-0

Chromosome-length genome assembly of Teladorsagia circumcincta - a globally important helminth parasite in livestock

BMC Genomics. 2023 Feb 15;24(1):74. doi: 10.1186/s12864-023-09172-0.

Authors

Shamshad Ul Hassan^{1

2}, Eng Guan Chua², Erwin A Paz^{1

2}, Chin Yen Tay², Johan C Greeff³, Dieter G Palmer³, Olga Dudchenko^{4

5}, Erez Lieberman Aiden^{4

5

6

7}, Graeme B Martin¹, Parwinder Kaur⁸

Affiliations

¹ UWA School of Agriculture and Environment, The University of Western Australia, 6009, Crawley, WA, Australia.
² Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.
³ Department of Primary Industries and Regional Development, Western Australia 3 Baron Hay Court, South Perth, 6151, WA, Australia.
⁴ The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, 77030, Houston, TX, USA.
⁵ Center for Theoretical Biological Physics, Rice University, 77005, Houston, TX, USA.
⁶ Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, China.
⁷ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁸ UWA School of Agriculture and Environment, The University of Western Australia, 6009, Crawley, WA, Australia. parwinder.kaur@uwa.edu.au.

Abstract

Background: Gastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta, infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta, such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics.

Results: We have constructed a high-quality reference genome, with chromosome-length scaffolds, by purging alternative haplotypes from the existing draft genome assembly and scaffolding the result using chromosome conformation, capture-based, in situ Hi-C technique. The improved (Hi-C) assembly resulted in six chromosome-length scaffolds with length ranging from 66.6 Mbp to 49.6 Mbp, 35% fewer sequences and reduction in size. Substantial improvements were also achieved in both the values for N50 (57.1 Mbp) and L50 (5 Mbp). A higher and comparable level of genome and proteome completeness was achieved for Hi-C assembly on BUSCO parameters. The Hi-C assembly had a greater synteny and number of orthologs with a closely related nematode, Haemonchus contortus.

Conclusion: This improved genomic resource is suitable as a foundation for the identification of potential targets for vaccine and drug development.

Keywords: 3D-DNA; Bioinformatics; Brown stomach worm; Genome assembly; Hi-C sequencing; Teladorsagia circumcincta.

MeSH terms

Animals
Genomics
Haemonchus*
Livestock
Nematoda*
Parasites*
Sheep
Sheep Diseases*

Grants and funding

UM1 HG009375/HG/NHGRI NIH HHS/United States