Urogenital blood fluke (Schistosoma haematobium)

S. haematobium prefers to migrate to blood vessels surrounding the bladder and genitals. Disease results principally from a chronic inflammatory process directed at schistosome eggs that become entrapped in urogenital tissues, and is often accompanied by increased susceptibility to HIV/AIDS in women or by malignant bladder cancer. Read more about urinary blood flukes on Wikipedia.

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Histopathology of Schistosomiasis haematobia by Dr. Edwin P. Ewing, Jr. (CDC), [Public Domain], via wikimedia.org

Chromosome-length genome assembly

Download the SciHae_3.0_HiC.fasta.gz file containing the chromosome-length (2n=16) assembly of the urinary blood fluke genome. All modifications with respect to the draft (see below) are annotated in the SciHae_3.0_HiC.assembly file. Some basic stats associated with the new reference, SciHae_3.0_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
409,407,418
847
3,324,407
19,645,000
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
409,856,863
563
48,184,357
92,473,630
Draft

The chromosome-length genome assembly is based on the draft assembly SciHae_3.0, credited below.

The draft assembly was generated by Neil Young, Andreas Stroehlein, Pasi Korhnonen and Robin Gasser at the University of Melbourne. The draft genome assembly was created using existing short-read Illumina and Dovetail sequence libraries and new Oxford Nanopore long-read data. Genomic data was created with support from the National Health and Medical Council and Australian Research Council.

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 adult whole worms sample for in situ Hi-C preparation was obtained from Neil Young (University of Melbourne, Melbourne Veterinary School).

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.

The draft assembly was generated by Neil Young, Andreas Stroehlein, Pasi Korhnonen and Robin Gasser at the University of Melbourne. The draft genome assembly was created using existing short-read Illumina and Dovetail sequence libraries and new Oxford Nanopore long-read data. Genomic data was created with support from the National Health and Medical Council and Australian Research Council.

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.