Brown stomach worm (Teladorsagia circumcincta)

In cool, moist climates Teladorsagia circumcincta is the major economic parasite of small ruminants. Read more about brown stomach worms in Food Animal Practice (Fifth Edition).

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Photo credits: A/Prof. Peta L. Clode, Centre for Microscopy, Characterisation and Analysis, UWA

Chromosome-length genome assembly

Download the T_circumcincta.14.0.ec.cg.pg_purgehaplotigs_HiC.fasta.gz file containing the chromosome-length (2n=12) assembly of the brown stomach worm genome. All modifications with respect to the draft (see below) are annotated in the T_circumcincta.14.0.ec.cg.pg_purgehaplotigs_HiC.assembly file. Some basic stats associated with the new reference, T_circumcincta.14.0.ec.cg.pg_purgehaplotigs_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
481,425,019
173,174
3,928
98,345
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
593,209,506
52,507
57,133,369
66,586,561
Draft

The chromosome-length genome assembly is based on the draft assembly T_circumcincta.14.0.ec.cg.pg_purgehaplotigs (GCA_002352805.1 ), credited below.

Palevich,N., Maclean,P., Mitreva, M., Scott, R. and Leathwick, "The complete mitochondrial genome of the New Zealand parasitic roundworm Teladorsagia circumcincta (Trichostrongyloidea: Haemonchidae) field strain NZ_Teci_NP" https://www.tandfonline.com/doi/full/10.1080/23802359.2019.1660241.

Method

3D Assembly was performed using 3D-DNA pipeline (Dudchenko et al., Science, 2017). The genome was reviewed using Juicebox Assembly Tools  (Dudchenko et al., bioRxiv, 2018). See Methods for more information.

Hi-C sample

The whole worms sample for in situ Hi-C preparation was obtained from Graeme B Martin (The University of Western Australia).

Hi-C Contact maps

Hi-C data was aligned to the draft reference using Juicer (Durand, Shamim et al., Cell Systems, 2016), and contact maps visualizing the alignments with respect to the draft and the new reference were built using 3D-DNA (Dudchenko et al., Science, 2017). The contact maps can be explored below via Juicebox.js interactive tool (Robinson et al., Cell Systems, 2018). To explore the assembly in greater detail, please download the .hic and .assembly files from the data release folder and use Juicebox Assembly Tools  (Dudchenko et al., bioRxiv, 2018).

References

If you use this genome assembly in your research, please check that the conditions of use associated with the draft permit it, and acknowledge the following work.

Palevich,N., Maclean,P., Mitreva, M., Scott, R. and Leathwick, "The complete mitochondrial genome of the New Zealand parasitic roundworm Teladorsagia circumcincta (Trichostrongyloidea: Haemonchidae) field strain NZ_Teci_NP" https://www.tandfonline.com/doi/full/10.1080/23802359.2019.1660241.

Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95. https://doi.org/10.1126/science.aal3327.

Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.

Disclaimer

This is a work in progress. If you notice any discrepancies in the map or have data that confirms or contradicts the suggested reference, please email us at thednazoo@gmail.com or leave a comment on the Forum.